The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Yim, Won Cheol; Swain, Mia L.; Ma, Dongna; An, Hong; Bird, Kevin A.; Curdie, David D.; Wang, Samuel; Ham, Hyun Don; Luzuriaga-Neira, Agusto; Kirkwood, Jay S.; Hur, Manhoi; Solomon, Juan K. Q.; Harper, Jeffrey F.; Kosma, Dylan K.; Alvarez-Ponce, David; Cushman, John C.; Edger, Patrick P.; Mason, Annaliese S.; Pires, J. Chris; Tang, Haibao; Zhang, Xingtan

doi:10.1093/plcell/koac249

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Journal Article · 12 August 2022 · The Plant Cell

DOI:https://doi.org/10.1093/plcell/koac249· OSTI ID:2424634

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Abstract

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

Research Organization:: University of California, Riverside, CA (United States)

Sponsoring Organization:: USDOE

OSTI ID:: 2424634

Journal Information:: The Plant Cell, Journal Name: The Plant Cell Journal Issue: 11 Vol. 34; ISSN 1040-4651

Publisher:: American Society of Plant Biologists (ASPB)

Country of Publication:: United States

Language:: English

References (204)

Genetic Diversity of the Two Commercial Tetraploid Cotton Species in theGossypiumDiversity Reference Set Hinze, Lori L.; Gazave, Elodie; Gore, Michael A. Journal of Heredity, Vol. 107, Issue 3 https://doi.org/10.1093/jhered/esw004	journal	January 2016
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Wang, Y.; Tang, H.; DeBarry, J. D. Nucleic Acids Research, Vol. 40, Issue 7 https://doi.org/10.1093/nar/gkr1293	journal	January 2012
Alterations in the leaf lipidome of Brassica carinata under high-temperature stress Zoong Lwe, Zolian; Sah, Saroj; Persaud, Leelawatti BMC Plant Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s12870-021-03189-x	journal	September 2021
Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement Lu, Kun; Wei, Lijuan; Li, Xiaolong Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09134-9	journal	March 2019
Prospects for Brassica Carinata as an Oilseed crop in India Malik, R. S. Experimental Agriculture, Vol. 26, Issue 1 https://doi.org/10.1017/S0014479700015465	journal	January 1990
Introgressing Subgenome Components from Brassica rapa and B. carinata to B. juncea for Broadening Its Genetic Base and Exploring Intersubgenomic Heterosis Wei, Zili; Wang, Meng; Chang, Shihao Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01677	journal	November 2016
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium Hawkins, J. S.; Kim, H.; Nason, J. D. Genome Research, Vol. 16, Issue 10 https://doi.org/10.1101/gr.5282906	journal	October 2006
Nuclear DNA Amounts in Angiosperms: Progress, Problems and Prospects Bennett, M. D. Annals of Botany, Vol. 95, Issue 1 https://doi.org/10.1093/aob/mci003	journal	January 2005
Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun Khedikar, Yogendra; Clarke, Wayne E.; Chen, Lifeng Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-69255-w	journal	July 2020
Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus Lee, HueyTyng; Chawla, Harmeet Singh; Obermeier, Christian Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00496	journal	April 2020
Brassica carinata - a new molecular farming platform for delivering bio-industrial oil feedstocks: case studies of genetic modifications to improve very long-chain fatty acid and oil content in seeds Taylor, David C.; Falk, Kevin C.; Palmer, C. Don Biofuels, Bioproducts and Biorefining, Vol. 4, Issue 5 https://doi.org/10.1002/bbb.231	journal	August 2010
Bifurcation and Enhancement of Autonomous-Nonautonomous Retrotransposon Partnership through LTR Swapping in Soybean Du, Jianchang; Tian, Zhixi; Bowen, Nathan J. The Plant Cell, Vol. 22, Issue 1 https://doi.org/10.1105/tpc.109.068775	journal	January 2010
UniProt: a hub for protein information Consortium, UniPot Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212 https://doi.org/10.1093/nar/gku989	journal	October 2014
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2376-y	journal	October 2018
Assessing the environmental sustainability of biofuels Kazamia, Elena; Smith, Alison G. Trends in Plant Science, Vol. 19, Issue 10 https://doi.org/10.1016/j.tplants.2014.08.001	journal	October 2014
Brassica carinata-derived biodiesel production: economics, sustainability and policies. The Italian case Basili, Marcello; Rossi, Maria Alessandra Journal of Cleaner Production, Vol. 191 https://doi.org/10.1016/j.jclepro.2018.03.306	journal	August 2018
Promoter polymorphism in FAE1.1 and FAE1.2 genes associated with erucic acid content in Brassica juncea Saini, Navinder; Koramutla, Murali Krishna Molecular Breeding, Vol. 39, Issue 5 https://doi.org/10.1007/s11032-019-0971-x	journal	May 2019
Origin and evolution of the octoploid strawberry genome Edger, Patrick P.; Poorten, Thomas J.; VanBuren, Robert Nature Genetics, Vol. 51, Issue 3 https://doi.org/10.1038/s41588-019-0356-4	journal	February 2019
Interactions among proteins of floral MADS‐box genes in Nuphar pumila (Nymphaeaceae) and the most recent common ancestor of extant angiosperms help understand the underlying mechanisms of the origin of the flower Li, Lin; Yu, Xian‐Xian; Guo, Chun‐Ce Journal of Systematics and Evolution, Vol. 53, Issue 4 https://doi.org/10.1111/jse.12148	journal	April 2015
Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq‐based visualization He, Zhesi; Wang, Lihong; Harper, Andrea L. Plant Biotechnology Journal, Vol. 15, Issue 5 https://doi.org/10.1111/pbi.12657	journal	December 2016
Experimental investigation of the effect of fatty acids configuration, chain length, branching and degree of unsaturation on biodiesel fuel properties obtained from lauric oils, high-oleic and high-linoleic vegetable oil biomass Folayan, Adewale Johnson; Anawe, Paul Apeye Lucky; Aladejare, Adeyemi Emman Energy Reports, Vol. 5 https://doi.org/10.1016/j.egyr.2019.06.013	journal	November 2019
Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata Zhang, Wenshan; Hu, Dandan; Raman, Rosy Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00615	journal	April 2017
Role of xyloglucan in cotton (Gossypium hirsutum L.) fiber elongation of the short fiber mutant Ligon lintless-2 (Li) Naoumkina, Marina; Hinchliffe, Doug J.; Fang, David D. Gene, Vol. 626 https://doi.org/10.1016/j.gene.2017.05.042	journal	August 2017
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael Plant Bioinformatics https://doi.org/10.1007/978-1-4939-3167-5_2	book	January 2016
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection Yang, Jinghua; Liu, Dongyuan; Wang, Xiaowu Nature Genetics, Vol. 48, Issue 10 https://doi.org/10.1038/ng.3657	journal	September 2016
Repbase Update, a database of repetitive elements in eukaryotic genomes Bao, Weidong; Kojima, Kenji K.; Kohany, Oleksiy Mobile DNA, Vol. 6, Issue 1 https://doi.org/10.1186/s13100-015-0041-9	journal	June 2015
The Capsella rubella genome and the genomic consequences of rapid mating system evolution Slotte, Tanja; Hazzouri, Khaled M.; Ågren, J. Arvid Nature Genetics, Vol. 45, Issue 7 https://doi.org/10.1038/ng.2669	journal	June 2013
Cuticular Wax Accumulation Is Associated with Drought Tolerance in Wheat Near-Isogenic Lines Guo, Jun; Xu, Wen; Yu, Xiaocong Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01809	journal	November 2016
Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle Zhang, Yue; Yu, Zhe; Zheng, Chunfang Interface Focus, Vol. 11, Issue 4 https://doi.org/10.1098/rsfs.2020.0059	journal	June 2021
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data Zhang, Xingtan; Zhang, Shengcheng; Zhao, Qian Nature Plants, Vol. 5, Issue 8 https://doi.org/10.1038/s41477-019-0487-8	journal	August 2019
Genomic insights into the origin, domestication and diversification of Brassica juncea Kang, Lei; Qian, Lunwen; Zheng, Ming Nature Genetics, Vol. 53, Issue 9 https://doi.org/10.1038/s41588-021-00922-y	journal	September 2021
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations Campbell, Michael S.; Law, MeiYee; Holt, Carson Plant Physiology, Vol. 164, Issue 2 https://doi.org/10.1104/pp.113.230144	journal	December 2013
Characterization of FAE1 in the zero erucic acid germplasm of Brassica rapa L. Yan, Guixin; Li, Dan; Cai, Mengxian Breeding Science, Vol. 65, Issue 3 https://doi.org/10.1270/jsbbs.65.257	journal	January 2015
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome Chalhoub, B.; Denoeud, F.; Liu, S. Science, Vol. 345, Issue 6199 https://doi.org/10.1126/science.1253435	journal	August 2014
A chromosome‐scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes Paritosh, Kumar; Yadava, Satish Kumar; Singh, Priyansha Plant Biotechnology Journal, Vol. 19, Issue 3 https://doi.org/10.1111/pbi.13492	journal	December 2020
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice Rizzon, Carene; Ponger, Loic; Gaut, Brandon S. PLoS Computational Biology, Vol. 2, Issue 9 https://doi.org/10.1371/journal.pcbi.0020115	journal	January 2006
GOATOOLS: A Python library for Gene Ontology analyses Klopfenstein, D. V.; Zhang, Liangsheng; Pedersen, Brent S. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28948-z	journal	July 2018
The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing Hloušková, Petra; Mandáková, Terezie; Pouch, Milan Annals of Botany, Vol. 124, Issue 1 https://doi.org/10.1093/aob/mcz036	journal	April 2019
Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers Allender, Charlotte J.; King, Graham J. BMC Plant Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2229-10-54	journal	January 2010
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 49, Issue W1 https://doi.org/10.1093/nar/gkab301	journal	April 2021
The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers Cheng, Shifeng; van den Bergh, Erik; Zeng, Peng The Plant Cell, Vol. 25, Issue 8 https://doi.org/10.1105/tpc.113.113480	journal	August 2013
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database Brůna, Tomáš; Hoff, Katharina J.; Lomsadze, Alexandre NAR Genomics and Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1093/nargab/lqaa108	journal	January 2021
The Evolutionary Fate and Consequences of Duplicate Genes Lynch, M. Science, Vol. 290, Issue 5494 https://doi.org/10.1126/science.290.5494.1151	journal	November 2000
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt Molecular Biology and Evolution, Vol. 32, Issue 1 https://doi.org/10.1093/molbev/msu300	journal	November 2014
Tabix: fast retrieval of sequence features from generic TAB-delimited files Li, H. Bioinformatics, Vol. 27, Issue 5 https://doi.org/10.1093/bioinformatics/btq671	journal	January 2011
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression Hollister, J. D.; Gaut, B. S. Genome Research, Vol. 19, Issue 8 https://doi.org/10.1101/gr.091678.109	journal	May 2009
A Role for Gene Duplication and Natural Variation of Gene Expression in the Evolution of Metabolism Kliebenstein, Daniel J. PLoS ONE, Vol. 3, Issue 3 https://doi.org/10.1371/journal.pone.0001838	journal	March 2008
Differences in Osmoregulation in Brassica species Kumar, Ashok; Singh, P.; Singh, D. P. Annals of Botany, Vol. 54, Issue 4 https://doi.org/10.1093/oxfordjournals.aob.a086824	journal	October 1984
The causes and consequences of subgenome dominance in hybrids and recent polyploids Bird, Kevin A.; VanBuren, Robert; Puzey, Joshua R. New Phytologist, Vol. 220, Issue 1 https://doi.org/10.1111/nph.15256	journal	June 2018
Assessing the efficiency of changes in land use for mitigating climate change Searchinger, Timothy D.; Wirsenius, Stefan; Beringer, Tim Nature, Vol. 564, Issue 7735 https://doi.org/10.1038/s41586-018-0757-z	journal	December 2018
Analysis of the Molecular Basis of Flowering Time Variation in Arabidopsis Accessions Gazzani, Silvia; Gendall, Anthony R.; Lister, Clare Plant Physiology, Vol. 132, Issue 2 https://doi.org/10.1104/pp.103.021212	journal	June 2003
Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea Navabi, Zahra-Katy; Huebert, Terry; Sharpe, Andrew G. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-250	journal	April 2013
Rapid and Efficient Isolation of High Quality Nucleic Acids from Plant Tissues Rich in Polyphenols and Polysaccharides Japelaghi, Reza Heidari; Haddad, Raheem; Garoosi, Ghasem-Ali Molecular Biotechnology, Vol. 49, Issue 2 https://doi.org/10.1007/s12033-011-9384-8	journal	February 2011
Overexpression of BnKCS1-1, BnKCS1-2, and BnCER1-2 promotes cuticular wax production and increases drought tolerance in Brassica napus Wang, Yanmei; Jin, Shurong; Xu, Yi The Crop Journal, Vol. 8, Issue 1 https://doi.org/10.1016/j.cj.2019.04.006	journal	February 2020
Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus Huang, Shunmou; Deng, Linbin; Guan, Mei BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-717	journal	January 2013
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes Grabundzija, Ivana; Messing, Simon A.; Thomas, Jainy Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10716	journal	March 2016
Ethiopian Mustard (Brassica carinata A. Braun) as an Alternative Energy Source and Sustainable Crop Hagos, Rahiel; Shaibu, Abdulwahab Saliu; Zhang, Lei Sustainability, Vol. 12, Issue 18 https://doi.org/10.3390/su12187492	journal	September 2020
A high‐quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance Chen, Xuequn; Tong, Chaobo; Zhang, Xingtan Plant Biotechnology Journal, Vol. 19, Issue 3 https://doi.org/10.1111/pbi.13493	journal	November 2020
Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene Gupta, V.; Mukhopadhyay, A.; Arumugam, N. Theoretical and Applied Genetics, Vol. 108, Issue 4 https://doi.org/10.1007/s00122-003-1481-z	journal	October 2003
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds Dudchenko, Olga; Batra, Sanjit S.; Omer, Arina D. Science, Vol. 356, Issue 6333 https://doi.org/10.1126/science.aal3327	journal	March 2017
CPGAVAS2, an integrated plastome sequence annotator and analyzer Shi, Linchun; Chen, Haimei; Jiang, Mei Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz345	journal	May 2019
Impact of transposable elements on the organization and function of allopolyploid genomes: Research review Parisod, Christian; Alix, Karine; Just, Jérémy New Phytologist, Vol. 186, Issue 1 https://doi.org/10.1111/j.1469-8137.2009.03096.x	journal	December 2009
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed Qian, W.; Meng, J.; Li, M. Theoretical and Applied Genetics, Vol. 113, Issue 1 https://doi.org/10.1007/s00122-006-0269-3	journal	April 2006
Highly Expressed Genes in Yeast Evolve Slowly Pál, Csaba; Papp, Balázs; Hurst, Laurence D. Genetics, Vol. 158, Issue 2 https://doi.org/10.1093/genetics/158.2.927	journal	June 2001
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage Tang, H.; Bowers, J. E.; Wang, X. Proceedings of the National Academy of Sciences, Vol. 107, Issue 1 https://doi.org/10.1073/pnas.0908007107	journal	December 2009
Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution Mason, Annaliese S.; Wendel, Jonathan F. Frontiers in Genetics, Vol. 11 https://doi.org/10.3389/fgene.2020.01014	journal	August 2020
The meaning of Darwin's “abominable mystery” Friedman, William E. American Journal of Botany, Vol. 96, Issue 1 https://doi.org/10.3732/ajb.0800150	journal	January 2009
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G. Nature Genetics, Vol. 43, Issue 5 https://doi.org/10.1038/ng.807	journal	April 2011
Incorporating sequence quality data into alignment improves DNA read mapping Frith, Martin C.; Wan, Raymond; Horton, Paul Nucleic Acids Research, Vol. 38, Issue 7 https://doi.org/10.1093/nar/gkq010	journal	January 2010
Different Regulatory Regions Are Required for the Vernalization-Induced Repression of FLOWERING LOCUS C and for the Epigenetic Maintenance of Repression Sheldon, Candice C.; Conn, Anna B.; Dennis, Elizabeth S. The Plant Cell, Vol. 14, Issue 10 https://doi.org/10.1105/tpc.004564	journal	September 2002
DNA Methylation: Toward Crop Disease Resistance Improvement Tirnaz, Soodeh; Batley, Jacqueline Trends in Plant Science, Vol. 24, Issue 12 https://doi.org/10.1016/j.tplants.2019.08.007	journal	December 2019
Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication Wu, Xudong; Qi, Xiaoquan BMC Evolutionary Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2148-10-145	journal	January 2010
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement Walker, Bruce J.; Abeel, Thomas; Shea, Terrance PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0112963	journal	November 2014
Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize Morgante, Michele; Brunner, Stephan; Pea, Giorgio Nature Genetics, Vol. 37, Issue 9 https://doi.org/10.1038/ng1615	journal	July 2005
BRAD, the genetics and genomics database for Brassica plants Cheng, Feng; Liu, Shengyi; Wu, Jian BMC Plant Biology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2229-11-136	journal	January 2011
Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome Qian, Lunwen; Qian, Wei; Snowdon, Rod J. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-1170	journal	January 2014
Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy Pegueroles, Cinta; Laurie, Steve; Albà, M. Mar Molecular Biology and Evolution, Vol. 30, Issue 8 https://doi.org/10.1093/molbev/mst083	journal	April 2013
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure Kagale, Sateesh; Koh, Chushin; Nixon, John Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4706	journal	April 2014
Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize Schnable, James C.; Freeling, Michael PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0017855	journal	March 2011
RaGOO: fast and accurate reference-guided scaffolding of draft genomes Alonge, Michael; Soyk, Sebastian; Ramakrishnan, Srividya Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1829-6	journal	October 2019
The contribution of transposable elements to transcriptional novelty in plants: theFLCaffair Quadrana, Leandro Transcription, Vol. 11, Issue 3-4 https://doi.org/10.1080/21541264.2020.1803031	journal	August 2020
TimeTree: A Resource for Timelines, Timetrees, and Divergence Times Kumar, Sudhir; Stecher, Glen; Suleski, Michael Molecular Biology and Evolution, Vol. 34, Issue 7 https://doi.org/10.1093/molbev/msx116	journal	April 2017
The ‘effective number of codons’ used in a gene Wright, Frank Gene, Vol. 87, Issue 1 https://doi.org/10.1016/0378-1119(90)90491-9	journal	March 1990
Very-long-chain fatty acids (VLCFAs) in plant response to stress Zhukov, Anatoly V.; Shumskaya, Maria Functional Plant Biology, Vol. 47, Issue 8 https://doi.org/10.1071/FP19100	journal	January 2020
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants Qiao, Xin; Li, Qionghou; Yin, Hao Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1650-2	journal	February 2019
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events Bowers, John E.; Chapman, Brad A.; Rong, Junkang Nature, Vol. 422, Issue 6930 https://doi.org/10.1038/nature01521	journal	March 2003
Brassica carinata as an alternative oil crop for the production of biodiesel in Italy: agronomic evaluation, fuel production by transesterification and characterization Cardone, Massimo; Mazzoncini, Marco; Menini, Stefano Biomass and Bioenergy, Vol. 25, Issue 6 https://doi.org/10.1016/S0961-9534(03)00058-8	journal	December 2003
Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences Kim, Chang-Kug; Seol, Young-Joo; Perumal, Sampath Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-25585-4	journal	May 2018
A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics Lv, Honghao; Wang, Yong; Han, Fengqing Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-69389-x	journal	July 2020
Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus Samans, Birgit; Chalhoub, Boulos; Snowdon, Rod J. The Plant Genome, Vol. 10, Issue 3 https://doi.org/10.3835/plantgenome2017.02.0013	journal	November 2017
Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation Baduel, Pierre; Quadrana, Leandro; Hunter, Ben Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13730-0	journal	December 2019
Linkage disequilibrium and population structure in a core collection of Brassica napus (L.) Rahman, Mukhlesur; Hoque, Ahasanul; Roy, Jayanta PLOS ONE, Vol. 17, Issue 3 https://doi.org/10.1371/journal.pone.0250310	journal	March 2022
Helitron-like transposons contributed to the mating system transition from out-crossing to self-fertilizing in polyploid Brassica napus L. Gao, Changbin; Zhou, Guilong; Ma, Chaozhi Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep33785	journal	September 2016
The butterfly plant arms-race escalated by gene and genome duplications Edger, Patrick P.; Heidel-Fischer, Hanna M.; Bekaert, Michaël Proceedings of the National Academy of Sciences, Vol. 112, Issue 27 https://doi.org/10.1073/pnas.1503926112	journal	June 2015
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization Wolff, Joachim; Rabbani, Leily; Gilsbach, Ralf Nucleic Acids Research, Vol. 48, Issue W1 https://doi.org/10.1093/nar/gkaa220	journal	April 2020
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Ming, Ray; Hou, Shaobin; Feng, Yun Nature, Vol. 452, Issue 7190 https://doi.org/10.1038/nature06856	journal	April 2008
Twelve years of SAMtools and BCFtools Danecek, Petr; Bonfield, James K.; Liddle, Jennifer GigaScience, Vol. 10, Issue 2 https://doi.org/10.1093/gigascience/giab008	journal	January 2021
Synteny and Collinearity in Plant Genomes Tang, H.; Bowers, J. E.; Wang, X. Science, Vol. 320, Issue 5875 https://doi.org/10.1126/science.1153917	journal	April 2008
Genome sequencing supports a multi-vertex model for Brassiceae species Cheng, Feng; Liang, Jianli; Cai, Chengcheng Current Opinion in Plant Biology, Vol. 36 https://doi.org/10.1016/j.pbi.2017.01.006	journal	April 2017
Gene retention, fractionation and subgenome differences in polyploid plants Cheng, Feng; Wu, Jian; Cai, Xu Nature Plants, Vol. 4, Issue 5 https://doi.org/10.1038/s41477-018-0136-7	journal	April 2018
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps Belser, Caroline; Istace, Benjamin; Denis, Erwan Nature Plants, Vol. 4, Issue 11 https://doi.org/10.1038/s41477-018-0289-4	journal	November 2018
AUGUSTUS: ab initio prediction of alternative transcripts Stanke, M.; Keller, O.; Gunduz, I. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl200	journal	July 2006
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes Cantarel, B. L.; Korf, I.; Robb, S. M. C. Genome Research, Vol. 18, Issue 1 https://doi.org/10.1101/gr.6743907	journal	November 2007
Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies Zhang, Lei; Cai, Xu; Wu, Jian Horticulture Research, Vol. 5, Issue 1 https://doi.org/10.1038/s41438-018-0071-9	journal	August 2018
Patterns of Nucleotide Substitution Among Simultaneously Duplicated Gene Pairs in Arabidopsis thaliana Zhang, Liqing; Vision, Todd J.; Gaut, Brandon S. Molecular Biology and Evolution, Vol. 19, Issue 9 https://doi.org/10.1093/oxfordjournals.molbev.a004209	journal	September 2002
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes Thomas, B. C. Genome Research, Vol. 16, Issue 7 https://doi.org/10.1101/gr.4708406	journal	July 2006
Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes Feschotte, C.; Wessler, S. R. Proceedings of the National Academy of Sciences, Vol. 98, Issue 16 https://doi.org/10.1073/pnas.171326198	journal	July 2001
Evolution of crop species: genetics of domestication and diversification Meyer, Rachel S.; Purugganan, Michael D. Nature Reviews Genetics, Vol. 14, Issue 12 https://doi.org/10.1038/nrg3605	journal	November 2013
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.215087.116	journal	March 2017
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation Willing, Eva-Maria; Rawat, Vimal; Mandáková, Terezie Nature Plants, Vol. 1, Issue 2 https://doi.org/10.1038/nplants.2014.23	journal	February 2015
A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome Perumal, Sampath; Koh, Chu Shin; Jin, Lingling Nature Plants, Vol. 6, Issue 8 https://doi.org/10.1038/s41477-020-0735-y	journal	August 2020
Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes Cai, Xu; Wu, Jian; Liang, Jianli Theoretical and Applied Genetics, Vol. 133, Issue 11 https://doi.org/10.1007/s00122-020-03664-3	journal	August 2020
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis Bioinformatics, Vol. 31, Issue 19 https://doi.org/10.1093/bioinformatics/btv351	journal	June 2015
Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa Boutte, Julien; Maillet, Loeiz; Chaussepied, Thomas Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.577536	journal	November 2020
Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize Barbaglia, Allison M.; Klusman, Katarina M.; Higgins, John Genetics, Vol. 190, Issue 3 https://doi.org/10.1534/genetics.111.136176	journal	December 2011
The population genomics of adaptive loss of function Monroe, J. Grey; McKay, John K.; Weigel, Detlef Heredity, Vol. 126, Issue 3 https://doi.org/10.1038/s41437-021-00403-2	journal	February 2021
Araport: the Arabidopsis Information Portal Krishnakumar, Vivek; Hanlon, Matthew R.; Contrino, Sergio Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1200	journal	November 2014
Detectingde NovoHomoeologous Recombination Events in CultivatedBrassica napusUsing a Genome-Wide SNP Array Higgins, Erin E.; Clarke, Wayne E.; Howell, Elaine C. G3 Genes\|Genomes\|Genetics, Vol. 8, Issue 8 https://doi.org/10.1534/g3.118.200118	journal	August 2018
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza: Evolutionary dynamics of ancient retrotransposon family Ammiraju, Jetty S. S.; Zuccolo, Andrea; Yu, Yeisoo The Plant Journal, Vol. 52, Issue 2 https://doi.org/10.1111/j.1365-313X.2007.03242.x	journal	August 2007
Homoeologous recombination in allopolyploids: the polyploid ratchet: Research review Gaeta, Robert T.; Chris Pires, J. New Phytologist, Vol. 186, Issue 1 https://doi.org/10.1111/j.1469-8137.2009.03089.x	journal	December 2009
Genomic Plasticity and the Diversity of Polyploid Plants Leitch, A. R.; Leitch, I. J. Science, Vol. 320, Issue 5875 https://doi.org/10.1126/science.1153585	journal	April 2008
Genes of ACYL CARRIER PROTEIN Family Show Different Expression Profiles and Overexpression of ACYL CARRIER PROTEIN 5 Modulates Fatty Acid Composition and Enhances Salt Stress Tolerance in Arabidopsis Huang, Jiexue; Xue, Caiwen; Wang, Han Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00987	journal	June 2017
Transposable elements contribute to dynamic genome content in maize Anderson, Sarah N.; Stitzer, Michelle C.; Brohammer, Alex B. The Plant Journal, Vol. 100, Issue 5 https://doi.org/10.1111/tpj.14489	journal	September 2019
Non‐random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization Nicolas, Stéphane D.; Monod, Hervé; Eber, Frédérique The Plant Journal, Vol. 70, Issue 4 https://doi.org/10.1111/j.1365-313X.2012.04914.x	journal	March 2012
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Besemer, J.; Borodovsky, M. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki487	journal	July 2005
Yesterday's polyploids and the mystery of diploidization Wolfe, Kenneth H. Nature Reviews Genetics, Vol. 2, Issue 5 https://doi.org/10.1038/35072009	journal	May 2001
Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus Wu, Jian; Lin, Li; Xu, Meiling BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4966-5	journal	August 2018
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Dating the origins of polyploidy events Doyle, Jeff J.; Egan, Ashley N. New Phytologist, Vol. 186, Issue 1 https://doi.org/10.1111/j.1469-8137.2009.03118.x	journal	December 2009
Gene Fractionation and Function in the Ancient Subgenomes of Maize Renny-Byfield, Simon; Rodgers-Melnick, Eli; Ross-Ibarra, Jeffrey Molecular Biology and Evolution, Vol. 34, Issue 8 https://doi.org/10.1093/molbev/msx121	journal	April 2017
The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype Sun, Fengming; Fan, Guangyi; Hu, Qiong The Plant Journal, Vol. 92, Issue 3 https://doi.org/10.1111/tpj.13669	journal	October 2017
Plant fatty acyl reductases: Enzymes generating fatty alcohols for protective layers with potential for industrial applications Rowland, Owen; Domergue, Frédéric Plant Science, Vol. 193-194 https://doi.org/10.1016/j.plantsci.2012.05.002	journal	September 2012
Insights into salt tolerance from the genome of Thellungiella salsuginea Wu, Hua-Jun; Zhang, Zhonghui; Wang, Jun-Yi Proceedings of the National Academy of Sciences, Vol. 109, Issue 30 https://doi.org/10.1073/pnas.1209954109	journal	July 2012
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions Haudry, Annabelle; Platts, Adrian E.; Vello, Emilio Nature Genetics, Vol. 45, Issue 8 https://doi.org/10.1038/ng.2684	journal	June 2013
Differential Activation of Partially Redundant Δ9 Stearoyl-ACP Desaturase Genes Is Critical for Omega-9 Monounsaturated Fatty Acid Biosynthesis During Seed Development in Arabidopsis Kazaz, Sami; Barthole, Guillaume; Domergue, Frédéric The Plant Cell, Vol. 32, Issue 11 https://doi.org/10.1105/tpc.20.00554	journal	September 2020
Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower Edger, Patrick P.; Smith, Ronald; McKain, Michael R. The Plant Cell, Vol. 29, Issue 9 https://doi.org/10.1105/tpc.17.00010	journal	August 2017
Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants Alix, Karine; Gérard, Pierre R.; Schwarzacher, Trude Annals of Botany, Vol. 120, Issue 2 https://doi.org/10.1093/aob/mcx079	journal	July 2017
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments Yim, Won Cheol; Cushman, John C. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3486	journal	June 2017
Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences Veeckman, Elisabeth; Ruttink, Tom; Vandepoele, Klaas The Plant Cell, Vol. 28, Issue 8 https://doi.org/10.1105/tpc.16.00349	journal	August 2016
Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop Lloyd, Andrew; Blary, Aurélien; Charif, Delphine New Phytologist, Vol. 217, Issue 1 https://doi.org/10.1111/nph.14836	journal	October 2017
OrthoFinder: phylogenetic orthology inference for comparative genomics Emms, David M.; Kelly, Steven Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1832-y	journal	November 2019
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity Lang, Daniel; Weiche, Benjamin; Timmerhaus, Gerrit Genome Biology and Evolution, Vol. 2 https://doi.org/10.1093/gbe/evq032	journal	January 2010
Polyphyletic origins of Brassica napus : new evidence based on organelle and nuclear RFLP analyses Song, Keming; Osborn, Thomas C. Genome, Vol. 35, Issue 6 https://doi.org/10.1139/g92-152	journal	December 1992
STAR: ultrafast universal RNA-seq aligner Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts635	journal	October 2012
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus Song, Jia-Ming; Guan, Zhilin; Hu, Jianlin Nature Plants, Vol. 6, Issue 1 https://doi.org/10.1038/s41477-019-0577-7	journal	January 2020
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea Parkin, Isobel AP; Koh, Chushin; Tang, Haibao Genome Biology, Vol. 15, Issue 6 https://doi.org/10.1186/gb-2014-15-6-r77	journal	January 2014
Chromosome triplication found across the tribe Brassiceae Lysak, M. A. Genome Research, Vol. 15, Issue 4 https://doi.org/10.1101/gr.3531105	journal	March 2005
Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus Stein, Anna; Coriton, Olivier; Rousseau-Gueutin, Mathieu Plant Biotechnology Journal, Vol. 15, Issue 11 https://doi.org/10.1111/pbi.12732	journal	April 2017
The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron: A fungal helitron includes a regulated promoter Cultrone, Antonietta; Domínguez, Yazmid Reyes; Drevet, Christine Molecular Microbiology, Vol. 63, Issue 6 https://doi.org/10.1111/j.1365-2958.2007.05609.x	journal	January 2007
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa Qi, Xinshuai; An, Hong; Hall, Tara E. New Phytologist, Vol. 230, Issue 1 https://doi.org/10.1111/nph.17194	journal	March 2021
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus Bird, Kevin A.; Niederhuth, Chad E.; Ou, Shujun New Phytologist, Vol. 230, Issue 1 https://doi.org/10.1111/nph.17137	journal	January 2021
Chromosome level comparative analysis of Brassica genomes Wang, Wenliang; Guan, Rui; Liu, Xing Plant Molecular Biology, Vol. 99, Issue 3 https://doi.org/10.1007/s11103-018-0814-x	journal	January 2019
Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence Arias, Tatiana; Beilstein, Mark A.; Tang, Michelle American Journal of Botany, Vol. 101, Issue 1 https://doi.org/10.3732/ajb.1300312	journal	January 2014
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock Sanderson, M. J. Bioinformatics, Vol. 19, Issue 2 https://doi.org/10.1093/bioinformatics/19.2.301	journal	January 2003
Regulation of FATTY ACID ELONGATION1 expression in embryonic and vascular tissues of Brassica napus Chiron, Hélène; Wilmer, Jeroen; Lucas, Marie-Odile Plant Molecular Biology, Vol. 88, Issue 1-2 https://doi.org/10.1007/s11103-015-0309-y	journal	March 2015
Draft Sequences of the Radish (Raphanus sativus L.) Genome Kitashiba, Hiroyasu; Li, Feng; Hirakawa, Hideki DNA Research, Vol. 21, Issue 5 https://doi.org/10.1093/dnares/dsu014	journal	May 2014
The Reference Genome of the Halophytic Plant Eutrema salsugineum Yang, Ruolin; Jarvis, David E.; Chen, Hao Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00046	journal	January 2013
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing Servant, Nicolas; Varoquaux, Nelle; Lajoie, Bryan R. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0831-x	journal	December 2015
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Haas, B. J. Nucleic Acids Research, Vol. 31, Issue 19 https://doi.org/10.1093/nar/gkg770	journal	October 2003
Coordinate Regulation of the Nuclear and Plastidic Genes Coding for the Subunits of the Heteromeric Acetyl-Coenzyme A Carboxylase Ke, Jinshan; Wen, Tuan-Nan; Nikolau, Basil J. Plant Physiology, Vol. 122, Issue 4 https://doi.org/10.1104/pp.122.4.1057	journal	April 2000
Enhancer activity ofHelitroninsericin-1gene promoter fromBombyx mori Huang, Ke; Li, Chun-Feng; Wu, Jie Insect Science, Vol. 23, Issue 3 https://doi.org/10.1111/1744-7917.12347	journal	May 2016
Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy Waminal, Nomar Espinosa; Pellerin, Remnyl Joyce; Kang, Sang-Ho Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.629898	journal	February 2021
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly Xu, Gui-Cai; Xu, Tian-Jun; Zhu, Rui GigaScience, Vol. 8, Issue 1 https://doi.org/10.1093/gigascience/giy157	journal	December 2018
Ab initio Gene Finding in Drosophila Genomic DNA Salamov, Asaf A.; Solovyev, Victor V. Genome Research, Vol. 10, Issue 4, p. 516-522 https://doi.org/10.1101/gr.10.4.516	journal	April 2000
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla No authors listed Nature, Vol. 449, Issue 7161, p. 463-467 https://doi.org/10.1038/nature06148	journal	August 2007
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments Suyama, M.; Torrents, D.; Bork, P. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl315	journal	July 2006
The important contribution of transposable elements to phenotypic variation and evolution Catlin, Nathan S.; Josephs, Emily B. Current Opinion in Plant Biology, Vol. 65 https://doi.org/10.1016/j.pbi.2021.102140	journal	February 2022
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants Freeling, Michael; Woodhouse, Margaret R.; Subramaniam, Shabarinath Current Opinion in Plant Biology, Vol. 15, Issue 2 https://doi.org/10.1016/j.pbi.2012.01.015	journal	April 2012
Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes Palazzo, Antonio; Lorusso, Patrizio; Miskey, Csaba Mobile DNA, Vol. 10, Issue 1 https://doi.org/10.1186/s13100-019-0155-6	journal	April 2019
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss Schnable, J. C.; Springer, N. M.; Freeling, M. Proceedings of the National Academy of Sciences, Vol. 108, Issue 10 https://doi.org/10.1073/pnas.1101368108	journal	February 2011
Enhancement of growth by expression of poplar cellulase in Arabidopsis thaliana Park, Yong Woo; Tominaga, Rumi; Sugiyama, Junji The Plant Journal, Vol. 33, Issue 6 https://doi.org/10.1046/j.1365-313X.2003.01696.x	journal	March 2003
The genome of Theobroma cacao Argout, Xavier; Salse, Jerome; Aury, Jean-Marc Nature Genetics, Vol. 43, Issue 2 https://doi.org/10.1038/ng.736	journal	December 2010
Gene capture by transposable elements leads to epigenetic conflict in maize Muyle, Aline; Seymour, Danelle; Darzentas, Nikos Molecular Plant, Vol. 14, Issue 2 https://doi.org/10.1016/j.molp.2020.11.003	journal	February 2021
Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica Song, Xiaoming; Wei, Yanping; Xiao, Dong Plant Physiology, Vol. 186, Issue 1 https://doi.org/10.1093/plphys/kiab048	journal	February 2021
Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species Healey, Adam; Furtado, Agnelo; Cooper, Tal Plant Methods, Vol. 10, Issue 1 https://doi.org/10.1186/1746-4811-10-21	journal	January 2014
Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus Li, Mengdi; Wang, Ruihua; Wu, Xiaoming BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6747-1	journal	April 2020
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes Ranallo-Benavidez, T. Rhyker; Jaron, Kamil S.; Schatz, Michael C. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14998-3	journal	March 2020
Maternal Inheritance of U’s Triangle and Evolutionary Process of Brassica Mitochondrial Genomes Xue, Jia-Yu; Wang, Yue; Chen, Min Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00805	journal	June 2020
Very-long-chain fatty acid biosynthesis is controlled through the expression and specificity of the condensing enzyme Millar, Anthony A.; Kunst, Ljerka The Plant Journal, Vol. 12, Issue 1 https://doi.org/10.1046/j.1365-313X.1997.12010121.x	journal	July 1997
Transposable elements and the plant pan-genomes Morgante, M.; Depaoli, E.; Radovic, S. Current Opinion in Plant Biology, Vol. 10, Issue 2 https://doi.org/10.1016/j.pbi.2007.02.001	journal	April 2007
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus An, Hong; Qi, Xinshuai; Gaynor, Michelle L. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10757-1	journal	June 2019
Enhancement of growth and cellulose accumulation by overexpression of xyloglucanase in poplar Park, Yong Woo; Baba, Kei'ichi; Furuta, Yuzo FEBS Letters, Vol. 564, Issue 1-2, p. 183-187 https://doi.org/10.1016/S0014-5793(04)00346-1	journal	March 2004
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution Huang, Gai; Wu, Zhiguo; Percy, Richard G. Nature Genetics, Vol. 52, Issue 5 https://doi.org/10.1038/s41588-020-0607-4	journal	April 2020
Helitron and CACTA DNA transposons actively reshape the common wheat - AK58 genome Wang, Zhiyong; Zhao, Guangyao; Yang, Qinghua Genomics, Vol. 114, Issue 2 https://doi.org/10.1016/j.ygeno.2022.110288	journal	March 2022
Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications Hu, Yanting; Wu, Xiaopei; Jin, Guihua Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.772655	journal	January 2022
Homoeologs: What Are They and How Do We Infer Them? Glover, Natasha M.; Redestig, Henning; Dessimoz, Christophe Trends in Plant Science, Vol. 21, Issue 7 https://doi.org/10.1016/j.tplants.2016.02.005	journal	July 2016
Long-read assembly of the Brassica napus reference genome Darmor-bzh Rousseau-Gueutin, Mathieu; Belser, Caroline; Da Silva, Corinne GigaScience, Vol. 9, Issue 12 https://doi.org/10.1093/gigascience/giaa137	journal	December 2020
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
Evolution by Gene Duplication Ohno, Susumu Springer Berlin, Heidelberg https://doi.org/10.1007/978-3-642-86659-3	book	January 1970
Gene finding in novel genomes Korf, Ian BMC Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2105-5-59	journal	May 2004
Organelle genome resources at NCBI Wolfsberg, Tyra G.; Schafer, Susan; Tatusov, Roman L. Trends in Biochemical Sciences, Vol. 26, Issue 3 https://doi.org/10.1016/S0968-0004(00)01773-4	journal	March 2001
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
Transposable Element Insertion and Epigenetic Modification Cause the Multiallelic Variation in the Expression of FAE1 in Sinapis alba Zeng, Fangqin; Cheng, Bifang The Plant Cell, Vol. 26, Issue 6 https://doi.org/10.1105/tpc.114.126631	journal	June 2014
Gene Loss Predictably Drives Evolutionary Adaptation Helsen, Jana; Voordeckers, Karin; Vanderwaeren, Laura Molecular Biology and Evolution, Vol. 37, Issue 10 https://doi.org/10.1093/molbev/msaa172	journal	July 2020
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan Plant Physiology, Vol. 173, Issue 4 https://doi.org/10.1104/pp.16.01942	journal	February 2017

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