Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
Abstract
Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
- Authors:
-
[1];
[3];
[4];
[2];
[6];
[7];
[5];
[2];
[9]
- Michigan State Univ., East Lansing, MI (United States). Dept. of Horticulture; Michigan State Univ., East Lansing, MI (United States). Plant Resilience Inst.
- Univ. of Georgia, Athens, GA (United States). Dept. of Genetics
- Michigan State Univ., East Lansing, MI (United States). Dept. of Horticulture; Michigan State Univ., East Lansing, MI (United States). Plant Resilience Inst.; Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology
- Michigan State Univ., East Lansing, MI (United States). Dept. of Horticulture; Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology
- Donald Danforth Plant Science Center, St. Louis, MO (United States)
- Michigan State Univ., East Lansing, MI (United States). Dept. of Horticulture
- Rutgers Univ., New Brunswick, NJ (United States). Waksman Inst. of Microbiology
- Cornell Univ., Ithaca, NY (United States). Dept. of Plant Breeding and Genetics
- J. Craig Venter Institute, La Jolla, CA (United States)
- Publication Date:
- Research Org.:
- J. Craig Venter Institute, La Jolla, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1629986
- Grant/Contract Number:
- SC0012639
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES
Citation Formats
VanBuren, Robert, Man Wai, Ching, Wang, Xuewen, Pardo, Jeremy, Yocca, Alan E., Wang, Hao, Chaluvadi, Srinivasa R., Han, Guomin, Bryant, Douglas, Edger, Patrick P., Messing, Joachim, Sorrells, Mark E., Mockler, Todd C., Bennetzen, Jeffrey L., and Michael, Todd P. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. United States: N. p., 2020.
Web. doi:10.1038/s41467-020-14724-z.
VanBuren, Robert, Man Wai, Ching, Wang, Xuewen, Pardo, Jeremy, Yocca, Alan E., Wang, Hao, Chaluvadi, Srinivasa R., Han, Guomin, Bryant, Douglas, Edger, Patrick P., Messing, Joachim, Sorrells, Mark E., Mockler, Todd C., Bennetzen, Jeffrey L., & Michael, Todd P. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. United States. https://doi.org/10.1038/s41467-020-14724-z
VanBuren, Robert, Man Wai, Ching, Wang, Xuewen, Pardo, Jeremy, Yocca, Alan E., Wang, Hao, Chaluvadi, Srinivasa R., Han, Guomin, Bryant, Douglas, Edger, Patrick P., Messing, Joachim, Sorrells, Mark E., Mockler, Todd C., Bennetzen, Jeffrey L., and Michael, Todd P. Fri .
"Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff". United States. https://doi.org/10.1038/s41467-020-14724-z. https://www.osti.gov/servlets/purl/1629986.
@article{osti_1629986,
title = {Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff},
author = {VanBuren, Robert and Man Wai, Ching and Wang, Xuewen and Pardo, Jeremy and Yocca, Alan E. and Wang, Hao and Chaluvadi, Srinivasa R. and Han, Guomin and Bryant, Douglas and Edger, Patrick P. and Messing, Joachim and Sorrells, Mark E. and Mockler, Todd C. and Bennetzen, Jeffrey L. and Michael, Todd P.},
abstractNote = {Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.},
doi = {10.1038/s41467-020-14724-z},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United States},
year = {Fri Feb 14 00:00:00 EST 2020},
month = {Fri Feb 14 00:00:00 EST 2020}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Growing the lost crops of eastern North America's original agricultural system
journal, July 2017
- Mueller, Natalie G.; Fritz, Gayle J.; Patton, Paul
- Nature Plants, Vol. 3, Issue 7
Increasing homogeneity in global food supplies and the implications for food security
journal, March 2014
- Khoury, C. K.; Bjorkman, A. D.; Dempewolf, H.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 11
T’ef (Eragrostis tef) in Ancient Agricultural Systems of Highland Ethiopia
journal, November 2008
- D’Andrea, A. C.
- Economic Botany, Vol. 62, Issue 4
The system of crop intensification: reports from the field on improving agricultural production, food security, and resilience to climate change for multiple crops
journal, January 2014
- Abraham, Binju; Araya, Hailu; Berhe, Tareke
- Agriculture & Food Security, Vol. 3, Issue 1
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)
journal, January 2014
- Cannarozzi, Gina; Plaza-Wüthrich, Sonia; Esfeld, Korinna
- BMC Genomics, Vol. 15, Issue 1
The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16
journal, January 2003
- Ingram, Amanda L.; Doyle, Jeff J.
- American Journal of Botany, Vol. 90, Issue 1
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012
- Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
- Nature, Vol. 492, Issue 7429
The contribution of polyploidy to variation in Brassica species
journal, August 2004
- Osborn, Thomas C.
- Physiologia Plantarum, Vol. 121, Issue 4
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
journal, April 2012
- Freeling, Michael; Woodhouse, Margaret R.; Subramaniam, Shabarinath
- Current Opinion in Plant Biology, Vol. 15, Issue 2
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
journal, August 2014
- Chalhoub, B.; Denoeud, F.; Liu, S.
- Science, Vol. 345, Issue 6199
Origin and evolution of the octoploid strawberry genome
journal, February 2019
- Edger, Patrick P.; Poorten, Thomas J.; VanBuren, Robert
- Nature Genetics, Vol. 51, Issue 3
Chromosome studies in the grass subfamily Chloridoideae. II. An analysis of polyploidy
journal, November 2003
- Roodt, Rouvay; Spies, Johan J.
- TAXON, Vol. 52, Issue 4
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
journal, March 2017
- Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin
- Genome Research, Vol. 27, Issue 5
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014
- Walker, Bruce J.; Abeel, Thomas; Shea, Terrance
- PLoS ONE, Vol. 9, Issue 11
A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]
journal, August 2006
- Yu, Ju-Kyung; Kantety, Ramesh V.; Graznak, Elizabeth
- Theoretical and Applied Genetics, Vol. 113, Issue 6
Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome
journal, February 2016
- Gebre, Yohannes Gedamu; Bertolini, Edoardo; Pè, Mario Enrico
- BMC Plant Biology, Vol. 16, Issue 1
Dating the origins of polyploidy events
journal, December 2009
- Doyle, Jeff J.; Egan, Ashley N.
- New Phytologist, Vol. 186, Issue 1
The paleontology of intergene retrotransposons of maize
journal, September 1998
- SanMiguel, Phillip; Gaut, Brandon S.; Tikhonov, Alexander
- Nature Genetics, Vol. 20, Issue 1
A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum
journal, November 2018
- VanBuren, Robert; Wai, Ching Man; Keilwagen, Jens
- Plant Direct, Vol. 2, Issue 11
Genome sequencing and analysis of the model grass Brachypodium distachyon
journal, February 2010
- ,
- Nature, Vol. 463, Issue 7282, p. 763-768
Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties
journal, June 2017
- Hittalmani, Shailaja; Mahesh, H. B.; Shirke, Meghana Deepak
- BMC Genomics, Vol. 18, Issue 1
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
journal, July 2006
- Thomas, B. C.
- Genome Research, Vol. 16, Issue 7
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
journal, February 2011
- Schnable, J. C.; Springer, N. M.; Freeling, M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
The genome of the mesopolyploid crop species Brassica rapa
journal, August 2011
- Wang, Xiaowu; Wang, Hanzhong; Wang, Jun
- Nature Genetics, Vol. 43, Issue 10
mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat
journal, May 2014
- Li, Aili; Liu, Dengcai; Wu, Jun
- The Plant Cell, Vol. 26, Issue 5
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
journal, February 2015
- Douglas, Gavin M.; Gos, Gesseca; Steige, Kim A.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 9
Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes
journal, October 2017
- Sun, Honghe; Wu, Shan; Zhang, Guoyu
- Molecular Plant, Vol. 10, Issue 10
Teff, an Orphan Cereal in the Chloridoideae , Provides Insights into the Evolution of Storage Proteins in Grasses
journal, May 2016
- Zhang, Wei; Xu, Jianhong; Bennetzen, Jeffrey L.
- Genome Biology and Evolution, Vol. 8, Issue 6
The transcriptional landscape of polyploid wheat
journal, August 2018
- Ramírez-González, R. H.; Borrill, P.; Lang, D.
- Science, Vol. 361, Issue 6403
Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus
journal, March 2010
- Buggs, Richard J. A.; Elliott, Natalie M.; Zhang, Linjing
- New Phytologist, Vol. 186, Issue 1
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense
journal, December 2018
- Wang, Maojun; Tu, Lili; Yuan, Daojun
- Nature Genetics, Vol. 51, Issue 2
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton
journal, March 2019
- Hu, Yan; Chen, Jiedan; Fang, Lei
- Nature Genetics, Vol. 51, Issue 4
Musa balbisiana genome reveals subgenome evolution and functional divergence
journal, July 2019
- Wang, Zhuo; Miao, Hongxia; Liu, Juhua
- Nature Plants, Vol. 5, Issue 8
Homoeologous recombination in allopolyploids: the polyploid ratchet: Research review
journal, December 2009
- Gaeta, Robert T.; Chris Pires, J.
- New Phytologist, Vol. 186, Issue 1
Recently Formed Polyploid Plants Diversify at Lower Rates
journal, August 2011
- Mayrose, I.; Zhan, S. H.; Rothfels, C. J.
- Science, Vol. 333, Issue 6047
Oligocene CO2 Decline Promoted C4 Photosynthesis in Grasses
journal, January 2008
- Christin, Pascal-Antoine; Besnard, Guillaume; Samaritani, Emanuela
- Current Biology, Vol. 18, Issue 1
The age of the grasses and clusters of origins of C 4 photosynthesis
journal, December 2008
- Vicentini, Alberto; Barber, Janet C.; Aliscioni, Sandra S.
- Global Change Biology, Vol. 14, Issue 12
Genetic Control of the Cytologically Diploid Behaviour of Hexaploid Wheat
journal, September 1958
- Riley, Ralph; Chapman, Victor
- Nature, Vol. 182, Issue 4637
High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis
journal, August 2012
- Zhu, Qihui; Smith, Shavannor M.; Ayele, Mulu
- Genetics, Vol. 192, Issue 3
Preparation of megabase-size DNA from plant nuclei
journal, January 1995
- Zhang, Hong-Bin; Zhao, Xinping; Ding, Xiaoling
- The Plant Journal, Vol. 7, Issue 1
Bandage: interactive visualization of de novo genome assemblies: Fig. 1.
journal, June 2015
- Wick, Ryan R.; Schultz, Mark B.; Zobel, Justin
- Bioinformatics, Vol. 31, Issue 20
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014
- Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei
- PLoS ONE, Vol. 9, Issue 2
Construction of integrated genetic linkage maps by means of a new computer package: Join Map
journal, May 1993
- Stam, Piet
- The Plant Journal, Vol. 3, Issue 5
MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
journal, October 1987
- Lander, Eric S.; Green, Philip; Abrahamson, Jeff
- Genomics, Vol. 1, Issue 2
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
journal, July 2016
- Durand, Neva C.; Shamim, Muhammad S.; Machol, Ido
- Cell Systems, Vol. 3, Issue 1
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
journal, March 2017
- Dudchenko, Olga; Batra, Sanjit S.; Omer, Arina D.
- Science, Vol. 356, Issue 6333
ALLMAPS: robust scaffold ordering based on multiple maps
journal, January 2015
- Tang, Haibao; Zhang, Xingtan; Miao, Chenyong
- Genome Biology, Vol. 16, Issue 1
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons
journal, December 2017
- Ou, Shujun; Jiang, Ning
- Plant Physiology, Vol. 176, Issue 2
Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes
journal, September 2011
- Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff
- The Plant Cell, Vol. 23, Issue 9
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes
journal, September 2009
- Rho, M.; Tang, H.
- Nucleic Acids Research, Vol. 37, Issue 21
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
journal, September 2010
- Han, Y.; Wessler, S. R.
- Nucleic Acids Research, Vol. 38, Issue 22
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
journal, October 2018
- Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo
- BMC Bioinformatics, Vol. 19, Issue 1
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes
journal, June 2014
- Xiong, W.; He, L.; Lai, J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 28
A unified classification system for eukaryotic transposable elements
journal, December 2007
- Wicker, Thomas; Sabot, François; Hua-Van, Aurélie
- Nature Reviews Genetics, Vol. 8, Issue 12
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
journal, January 2013
- Melters, Daniël P.; Bradnam, Keith R.; Young, Hugh A.
- Genome Biology, Vol. 14, Issue 1
Tandem repeats finder: a program to analyze DNA sequences
journal, January 1999
- Benson, G.
- Nucleic Acids Research, Vol. 27, Issue 2
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011
- Tamura, K.; Peterson, D.; Peterson, N.
- Molecular Biology and Evolution, Vol. 28, Issue 10
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
journal, December 2013
- Campbell, Michael S.; Law, MeiYee; Holt, Carson
- Plant Physiology, Vol. 164, Issue 2
STAR: ultrafast universal RNA-seq aligner
journal, October 2012
- Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix
- Bioinformatics, Vol. 29, Issue 1
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
journal, February 2015
- Pertea, Mihaela; Pertea, Geo M.; Antonescu, Corina M.
- Nature Biotechnology, Vol. 33, Issue 3
Gene prediction with a hidden Markov model and a new intron submodel
journal, September 2003
- Stanke, M.; Waack, S.
- Bioinformatics, Vol. 19, Issue Suppl 2
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015
- Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis
- Bioinformatics, Vol. 31, Issue 19
Near-optimal probabilistic RNA-seq quantification
journal, April 2016
- Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll
- Nature Biotechnology, Vol. 34, Issue 5
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
journal, July 2006
- Suyama, M.; Torrents, D.; Bork, P.
- Nucleic Acids Research, Vol. 34, Issue Web Server
A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum
journal, November 2018
- VanBuren, Robert; Wai, Ching Man; Keilwagen, Jens
- Plant Direct, Vol. 2, Issue 11
Estimation of nuclear DNA content of plants by flow cytometry
journal, August 1991
- Arumuganathan, K.; Earle, E. D.
- Plant Molecular Biology Reporter, Vol. 9, Issue 3
A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]
journal, August 2006
- Yu, Ju-Kyung; Kantety, Ramesh V.; Graznak, Elizabeth
- Theoretical and Applied Genetics, Vol. 113, Issue 6
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
journal, February 2020
- Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai
- Molecular Biology Reports, Vol. 47, Issue 3
T’ef (Eragrostis tef) in Ancient Agricultural Systems of Highland Ethiopia
journal, November 2008
- D’Andrea, A. C.
- Economic Botany, Vol. 62, Issue 4
MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
journal, October 1987
- Lander, Eric S.; Green, Philip; Abrahamson, Jeff
- Genomics, Vol. 1, Issue 2
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
journal, July 2016
- Durand, Neva C.; Shamim, Muhammad S.; Machol, Ido
- Cell Systems, Vol. 3, Issue 1
Oligocene CO2 Decline Promoted C4 Photosynthesis in Grasses
journal, January 2008
- Christin, Pascal-Antoine; Besnard, Guillaume; Samaritani, Emanuela
- Current Biology, Vol. 18, Issue 1
Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes
journal, October 2017
- Sun, Honghe; Wu, Shan; Zhang, Guoyu
- Molecular Plant, Vol. 10, Issue 10
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
journal, April 2012
- Freeling, Michael; Woodhouse, Margaret R.; Subramaniam, Shabarinath
- Current Opinion in Plant Biology, Vol. 15, Issue 2
The paleontology of intergene retrotransposons of maize
journal, September 1998
- SanMiguel, Phillip; Gaut, Brandon S.; Tikhonov, Alexander
- Nature Genetics, Vol. 20, Issue 1
Genetic Control of the Cytologically Diploid Behaviour of Hexaploid Wheat
journal, September 1958
- Riley, Ralph; Chapman, Victor
- Nature, Vol. 182, Issue 4637
Genome sequencing and analysis of the model grass Brachypodium distachyon
journal, February 2010
- ,
- Nature, Vol. 463, Issue 7282, p. 763-768
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012
- Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
- Nature, Vol. 492, Issue 7429
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
journal, February 2015
- Pertea, Mihaela; Pertea, Geo M.; Antonescu, Corina M.
- Nature Biotechnology, Vol. 33, Issue 3
Near-optimal probabilistic RNA-seq quantification
journal, April 2016
- Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll
- Nature Biotechnology, Vol. 34, Issue 5
The genome of the mesopolyploid crop species Brassica rapa
journal, August 2011
- Wang, Xiaowu; Wang, Hanzhong; Wang, Jun
- Nature Genetics, Vol. 43, Issue 10
Musa balbisiana genome reveals subgenome evolution and functional divergence
journal, July 2019
- Wang, Zhuo; Miao, Hongxia; Liu, Juhua
- Nature Plants, Vol. 5, Issue 8
Shared and distinct transcriptomic cell types across neocortical areas
journal, October 2018
- Tasic, Bosiljka; Yao, Zizhen; Graybuck, Lucas T.
- Nature, Vol. 563, Issue 7729
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense
journal, December 2018
- Wang, Maojun; Tu, Lili; Yuan, Daojun
- Nature Genetics, Vol. 51, Issue 2
Origin and evolution of the octoploid strawberry genome
journal, February 2019
- Edger, Patrick P.; Poorten, Thomas J.; VanBuren, Robert
- Nature Genetics, Vol. 51, Issue 3
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
journal, March 2021
- Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W.
- Nature Genetics, Vol. 53, Issue 3
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis
journal, September 2019
- Mandal, Malay; Okoreeh, Michael K.; Kennedy, Domenick E.
- Nature Immunology, Vol. 20, Issue 10
Acapsular Staphylococcus aureus with a non-functional agr regains capsule expression after passage through the bloodstream in a bacteremia mouse model
journal, August 2020
- Suligoy, Carlos M.; Díaz, Rocío E.; Gehrke, Ana-Katharina
- Scientific Reports, Vol. 10, Issue 1
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
journal, February 2011
- Schnable, J. C.; Springer, N. M.; Freeling, M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
Increasing homogeneity in global food supplies and the implications for food security
journal, March 2014
- Khoury, C. K.; Bjorkman, A. D.; Dempewolf, H.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 11
Gene prediction with a hidden Markov model and a new intron submodel
journal, September 2003
- Stanke, M.; Waack, S.
- Bioinformatics, Vol. 19, Issue Suppl 2
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015
- Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis
- Bioinformatics, Vol. 31, Issue 19
Bandage: interactive visualization of de novo genome assemblies: Fig. 1.
journal, June 2015
- Wick, Ryan R.; Schultz, Mark B.; Zobel, Justin
- Bioinformatics, Vol. 31, Issue 20
Teff, an Orphan Cereal in the Chloridoideae , Provides Insights into the Evolution of Storage Proteins in Grasses
journal, May 2016
- Zhang, Wei; Xu, Jianhong; Bennetzen, Jeffrey L.
- Genome Biology and Evolution, Vol. 8, Issue 6
Tandem repeats finder: a program to analyze DNA sequences
journal, January 1999
- Benson, G.
- Nucleic Acids Research, Vol. 27, Issue 2
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes
journal, September 2009
- Rho, M.; Tang, H.
- Nucleic Acids Research, Vol. 37, Issue 21
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
journal, September 2010
- Han, Y.; Wessler, S. R.
- Nucleic Acids Research, Vol. 38, Issue 22
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
journal, December 2013
- Campbell, Michael S.; Law, MeiYee; Holt, Carson
- Plant Physiology, Vol. 164, Issue 2
Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes
journal, September 2011
- Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff
- The Plant Cell, Vol. 23, Issue 9
Origin and Evolution of Diploid and Allopolyploid Camelina Genomes was Accompanied by Chromosome Shattering
journal, August 2019
- Mandáková, Terezie; Pouch, Milan; Brock, Jordan R.
- The Plant Cell
The age of the grasses and clusters of origins of C 4 photosynthesis
journal, December 2008
- Vicentini, Alberto; Barber, Janet C.; Aliscioni, Sandra S.
- Global Change Biology, Vol. 14, Issue 12
The contribution of polyploidy to variation in Brassica species
journal, August 2004
- Osborn, Thomas C.
- Physiologia Plantarum, Vol. 121, Issue 4
Dating the origins of polyploidy events
journal, December 2009
- Doyle, Jeff J.; Egan, Ashley N.
- New Phytologist, Vol. 186, Issue 1
Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus
journal, March 2010
- Buggs, Richard J. A.; Elliott, Natalie M.; Zhang, Linjing
- New Phytologist, Vol. 186, Issue 1
Recently Formed Polyploid Plants Diversify at Lower Rates
journal, August 2011
- Mayrose, I.; Zhan, S. H.; Rothfels, C. J.
- Science, Vol. 333, Issue 6047
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
journal, August 2014
- Chalhoub, B.; Denoeud, F.; Liu, S.
- Science, Vol. 345, Issue 6199
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
journal, March 2017
- Dudchenko, Olga; Batra, Sanjit S.; Omer, Arina D.
- Science, Vol. 356, Issue 6333
The transcriptional landscape of polyploid wheat
journal, August 2018
- Ramírez-González, R. H.; Borrill, P.; Lang, D.
- Science, Vol. 361, Issue 6403
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)
journal, January 2014
- Cannarozzi, Gina; Plaza-Wüthrich, Sonia; Esfeld, Korinna
- BMC Genomics, Vol. 15, Issue 1
The system of crop intensification: reports from the field on improving agricultural production, food security, and resilience to climate change for multiple crops
journal, January 2014
- Abraham, Binju; Araya, Hailu; Berhe, Tareke
- Agriculture & Food Security, Vol. 3, Issue 1
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
journal, October 2018
- Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo
- BMC Bioinformatics, Vol. 19, Issue 1
Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties
journal, June 2017
- Hittalmani, Shailaja; Mahesh, H. B.; Shirke, Meghana Deepak
- BMC Genomics, Vol. 18, Issue 1
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
ALLMAPS: robust scaffold ordering based on multiple maps
journal, January 2015
- Tang, Haibao; Zhang, Xingtan; Miao, Chenyong
- Genome Biology, Vol. 16, Issue 1
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014
- Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei
- PLoS ONE, Vol. 9, Issue 2
High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis
journal, August 2012
- Zhu, Qihui; Smith, Shavannor M.; Ayele, Mulu
- Genetics, Vol. 192, Issue 3
Chromosome studies in the grass subfamily Chloridoideae. II. An analysis of polyploidy
journal, November 2003
- Roodt, Rouvay; Spies, Johan J.
- TAXON, Vol. 52, Issue 4
GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing
journal, September 2016
- Wang, Xuewen; Wang, Le
- Frontiers in Plant Science, Vol. 7
The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16
journal, January 2003
- Ingram, Amanda L.; Doyle, Jeff J.
- American Journal of Botany, Vol. 90, Issue 1
Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution
text, January 2012
- Melters, Daniël P.; Bradnam, Keith R.; Young, Hugh A.
- arXiv
Works referencing / citing this record:
The divergence and positive selection of the plant‐specific BURP ‐containing protein family
journal, November 2015
- Wang, Lihui; Wu, Ningning; Zhu, Yan
- Ecology and Evolution, Vol. 5, Issue 22
Identification and expression of maebl, an erythrocyte-binding gene, in Plasmodium gallinaceum
journal, December 2012
- Martinez, Criseyda; Marzec, Timothy; Smith, Christopher D.
- Parasitology Research, Vol. 112, Issue 3
Evolutionary analysis of CBL-interacting protein kinase gene family in plants
journal, March 2013
- Ye, Chu-Yu; Xia, Xinli; Yin, Weilun
- Plant Growth Regulation, Vol. 71, Issue 1
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants
journal, June 2018
- Gazara, Rajesh K.; Moharana, Kanhu C.; Bellieny-Rabelo, Daniel
- Plant Molecular Biology, Vol. 97, Issue 4-5
Time-calibrated phylogenomics of the porcine epidemic diarrhea virus: genome-wide insights into the spatio-temporal dynamics
journal, April 2018
- Jang, Jisung; Yoon, Sook Hee; Lee, Wonseok
- Genes & Genomics, Vol. 40, Issue 8
Evolutionary signals of selection on cognition from the great tit genome and methylome
journal, January 2016
- Laine, Veronika N.; Gossmann, Toni I.; Schachtschneider, Kyle M.
- Nature Communications, Vol. 7, Issue 1
The pineapple genome and the evolution of CAM photosynthesis
journal, November 2015
- Ming, Ray; VanBuren, Robert; Wai, Ching Man
- Nature Genetics, Vol. 47, Issue 12
Evolutionary genomics of anthroponosis in Cryptosporidium
journal, March 2019
- Nader, Johanna L.; Mathers, Thomas C.; Ward, Ben J.
- Nature Microbiology, Vol. 4, Issue 5
Role of floral organ identity genes in the development of unisexual flowers of Quercus suber L.
journal, September 2017
- Sobral, Rómulo; Costa, M. Manuela R.
- Scientific Reports, Vol. 7, Issue 1
Genome-wide Identification of Jatropha curcas MAPK, MAPKK, and MAPKKK Gene Families and Their Expression Profile Under Cold Stress
journal, November 2018
- Wang, Haibo; Gong, Ming; Guo, Junyun
- Scientific Reports, Vol. 8, Issue 1
Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus
journal, November 2018
- Park, Jung Youn; Kim, Kwondo; Sohn, Hawsun
- Scientific Reports, Vol. 8, Issue 1
Expansion of viral variants associated with immune escape and impaired virion secretion in patients with HBV reactivation after resolved infection
journal, December 2018
- Inuzuka, Tadashi; Ueda, Yoshihide; Arasawa, Soichi
- Scientific Reports, Vol. 8, Issue 1
Evolutionary and Molecular Characterization of liver-enriched gene 1
journal, March 2020
- Dang, Yanna; Wang, Jin-Yang; Liu, Chen
- Scientific Reports, Vol. 10, Issue 1
Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution
journal, January 2016
- Lakhwani, Deepika; Pandey, Ashutosh; Dhar, Yogeshwar Vikram
- Scientific Reports, Vol. 6, Issue 1
Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet and their expression in rice
journal, April 2016
- Muthamilarasan, Mehanathan; Mangu, Venkata R.; Zandkarimi, Hana
- Scientific Reports, Vol. 6, Issue 1
The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus)
journal, June 2016
- Yue, Jia-Xing; Holland, Nicholas D.; Holland, Linda Z.
- Scientific Reports, Vol. 6, Issue 1
Identification of lipoxygenase (LOX) genes from legumes and their responses in wild type and cultivated peanut upon Aspergillus flavus infection
journal, October 2016
- Song, Hui; Wang, Pengfei; Li, Changsheng
- Scientific Reports, Vol. 6, Issue 1
Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing
journal, February 2017
- Kiran, Kanti; Rawal, Hukam C.; Dubey, Himanshu
- Scientific Reports, Vol. 7, Issue 1
Identification of a novel aminopolycarboxylic acid siderophore gene cluster encoding the biosynthesis of ethylenediaminesuccinic acid hydroxyarginine (EDHA)
journal, January 2018
- Spohn, Marius; Edenhart, Simone; Alanjary, Mohammad
- Metallomics, Vol. 10, Issue 5
Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution
journal, January 2011
- Fujii, S.; Bond, C. S.; Small, I. D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
Phylogenomics and the evolution of hemipteroid insects
journal, November 2018
- Johnson, Kevin P.; Dietrich, Christopher H.; Friedrich, Frank
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 50
Repertoires of G protein-coupled receptors for Ciona -specific neuropeptides
journal, April 2019
- Shiraishi, Akira; Okuda, Toshimi; Miyasaka, Natsuko
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 16
Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths
journal, October 2019
- Kawahara, Akito Y.; Plotkin, David; Espeland, Marianne
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 45
The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila
journal, March 2019
- Karr, Timothy L.; Southern, Helen; Rosenow, Matthew A.
- Molecular & Cellular Proteomics, Vol. 18
Draft genome sequence of an inbred line of Chenopodium quinoa , an allotetraploid crop with great environmental adaptability and outstanding nutritional properties
journal, July 2016
- Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo
- DNA Research, Vol. 23, Issue 6
Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster
journal, January 2012
- Campbell, Matthew A.; Rokas, Antonis; Slot, Jason C.
- Genome Biology and Evolution, Vol. 4, Issue 3
Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage
journal, September 2014
- Thomas, Jainy; Phillips, Caleb D.; Baker, Robert J.
- Genome Biology and Evolution, Vol. 6, Issue 10
Genome Evolution in the Primary Endosymbiont of Whiteflies Sheds Light on Their Divergence
journal, February 2015
- Santos-Garcia, Diego; Vargas-Chavez, Carlos; Moya, Andrés
- Genome Biology and Evolution, Vol. 7, Issue 3
Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling
journal, March 2016
- Jiang, Shu-Ye; Ramachandran, Srinivasan
- Genome Biology and Evolution, Vol. 8, Issue 4
Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome
journal, October 2018
- Lee, Chih-Chi; Wang, John
- Genome Biology and Evolution, Vol. 10, Issue 12
Deleterious Mutation Accumulation in Arabidopsis thaliana Pollen Genes: A Role for a Recent Relaxation of Selection
journal, June 2019
- Harrison, Mark C.; Mallon, Eamonn B.; Twell, Dave
- Genome Biology and Evolution, Vol. 11, Issue 7
Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats
journal, June 2020
- Gutiérrez-Guerrero, Yocelyn T.; Ibarra-Laclette, Enrique; Martínez del Río, Carlos
- GigaScience, Vol. 9, Issue 6
Genome sequence of Malania oleifera , a tree with great value for nervonic acid production
journal, January 2019
- Xu, Chao-Qun; Liu, Hui; Zhou, Shan-Shan
- GigaScience, Vol. 8, Issue 2
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China
journal, July 2019
- Yang, Jing; Wariss, Hafiz Muhammad; Tao, Lidan
- GigaScience, Vol. 8, Issue 7
Genomic evidence of neo-sex chromosomes in the eastern yellow robin
journal, September 2019
- Gan, Han Ming; Falk, Stephanie; Morales, Hernán E.
- GigaScience, Vol. 8, Issue 9
Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis
journal, August 2018
- Guillén, Yolanda; Casillas, Sònia; Ruiz, Alfredo
- Journal of Heredity, Vol. 110, Issue 1
Genomic Basis of Adaptive Evolution: The Survival of Amur Ide ( Leuciscu s waleckii ) in an Extremely Alkaline Environment
journal, October 2016
- Xu, Jian; Li, Jiong-Tang; Jiang, Yanliang
- Molecular Biology and Evolution, Vol. 34, Issue 1
Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING
journal, June 2014
- Wu, Xiaomei; Wu, Fei-Hua; Wang, Xiaoqiang
- Nucleic Acids Research, Vol. 42, Issue 13
Genome-Wide Identification, Evolution and Functional Divergence of MYB Transcription Factors in Chinese White Pear ( Pyrus bretschneideri )
journal, February 2016
- Li, Xiaolong; Xue, Cheng; Li, Jiaming
- Plant and Cell Physiology, Vol. 57, Issue 4
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
journal, July 2014
- Xi, Zhenxiang; Liu, Liang; Rest, Joshua S.
- Systematic Biology, Vol. 63, Issue 6
Ecological genomics of mutualism decline in nitrogen-fixing bacteria
journal, March 2016
- Klinger, Christie R.; Lau, Jennifer A.; Heath, Katy D.
- Proceedings of the Royal Society B: Biological Sciences, Vol. 283, Issue 1826
Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera
journal, February 2019
- Narayanan Kutty, Sujatha; Meusemann, Karen; Bayless, Keith M.
- Cladistics, Vol. 35, Issue 6
Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza: Genome evolution in polyploid Oryza
journal, May 2010
- Ammiraju, Jetty S. S.; Fan, Chuanzhu; Yu, Yeisoo
- The Plant Journal, Vol. 63, Issue 3
Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine: Metagenomic analysis of marine planktonic Thaumarchaea
journal, November 2011
- Tully, Benjamin J.; Nelson, William C.; Heidelberg, John F.
- Environmental Microbiology, Vol. 14, Issue 1
Timing of the Functional Diversification of α- and β-Adrenoceptors in Fish and Other Vertebrates
journal, April 2009
- Aris-Brosou, S.; Chen, X.; Perry, S. F.
- Annals of the New York Academy of Sciences, Vol. 1163, Issue 1
Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval
journal, July 2018
- Cai, Liming; Xi, Zhenxiang; Amorim, André M.
- New Phytologist, Vol. 221, Issue 1
Hybrid capture data unravel a rapid radiation of pimpliform parasitoid wasps (Hymenoptera: Ichneumonidae: Pimpliformes): Rapid radiation of pimpliform parasitoid wasps
journal, October 2018
- Klopfstein, Seraina; Langille, Barbara; Spasojevic, Tamara
- Systematic Entomology, Vol. 44, Issue 2
Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes
journal, October 2019
- Hsieh, PingHsun; Vollger, Mitchell R.; Dang, Vy
- Science, Vol. 366, Issue 6463
Host and Viral Determinants of Mx2 Antiretroviral Activity
journal, April 2014
- Busnadiego, Idoia; Kane, Melissa; Rihn, Suzannah J.
- Journal of Virology, Vol. 88, Issue 14
TRIM69 Inhibits Vesicular Stomatitis Indiana Virus
journal, October 2019
- Rihn, Suzannah J.; Aziz, Muhamad Afiq; Stewart, Douglas G.
- Journal of Virology, Vol. 93, Issue 20
Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus : From Genotype to Ecotype
journal, February 2019
- López-Pérez, Mario; Jayakumar, Jane M.; Haro-Moreno, Jose M.
- mBio, Vol. 10, Issue 1
Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits
journal, February 2017
- Castillo, Daniel; Alvise, Paul D.; Xu, Ruiqi
- mSystems, Vol. 2, Issue 1
Genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase I (FNSI) in Apiaceae
journal, February 2018
- Wang, Qi-Zhi; Downie, Stephen R.; Chen, Zhen-Xi
- Genome, Vol. 61, Issue 2
The WRKY Transcription Factor Genes in Lotus japonicus
journal, January 2014
- Song, Hui; Wang, Pengfei; Nan, Zhibiao
- International Journal of Genomics, Vol. 2014
Positive Selection of Squalene Synthase in Cucurbitaceae Plants
journal, May 2019
- Qian, Jieying; Liu, Yong; Ma, Chengtong
- International Journal of Genomics, Vol. 2019
Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice
journal, January 2019
- Wang, Bin; Li, Min; Yuan, Yijun
- Evolutionary Bioinformatics, Vol. 15
Phylogenomic analyses reveal a molecular signature linked to subterranean adaptation in rodents
journal, December 2015
- Du, Kang; Yang, Liandong; He, Shunping
- BMC Evolutionary Biology, Vol. 15, Issue 1
Analysis of the erythropoietin of a Tibetan Plateau schizothoracine fish (Gymnocypris dobula) reveals enhanced cytoprotection function in hypoxic environments
journal, January 2016
- Xu, Qianghua; Zhang, Chi; Zhang, Dongsheng
- BMC Evolutionary Biology, Vol. 16, Issue 1
Natriuretic peptides appeared after their receptors in vertebrates
journal, November 2019
- Grandchamp, Anna; Tahir, Shifa; Monget, Philippe
- BMC Evolutionary Biology, Vol. 19, Issue 1
Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis
journal, July 2015
- Patil, Gunvant; Valliyodan, Babu; Deshmukh, Rupesh
- BMC Genomics, Vol. 16, Issue 1
Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet
journal, October 2016
- Liu, Jia-Ming; Xu, Zhao-Shi; Lu, Pan-Pan
- BMC Genomics, Vol. 17, Issue 1
Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum
journal, February 2019
- Olarte, Rodrigo A.; Menke, Jon; Zhang, Ying
- BMC Genomics, Vol. 20, Issue 1
Genome-wide identification and interactome analysis of members of two-component system in Banana
journal, August 2019
- Dhar, Yogeshwar V.; Lakhwani, Deepika; Pandey, Ashutosh
- BMC Genomics, Vol. 20, Issue 1
Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts
journal, February 2020
- Tong, Wenjun; Li, Xiangchen; Wang, Entao
- BMC Genomics, Vol. 21, Issue 1
Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants
journal, February 2017
- Qian, Jieying; Liu, Yong; Chao, Naixia
- BMC Molecular Biology, Vol. 18, Issue 1
Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors
journal, October 2018
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- BMC Plant Biology, Vol. 18, Issue 1
The Extinction Dynamics of Bacterial Pseudogenes
journal, August 2010
- Kuo, Chih-Horng; Ochman, Howard
- PLoS Genetics, Vol. 6, Issue 8
Control of yeast retrotransposons mediated through nucleoporin evolution
journal, April 2018
- Rowley, Paul A.; Patterson, Kurt; Sandmeyer, Suzanne B.
- PLOS Genetics, Vol. 14, Issue 4
Evolutionary Genomics Reveals Lineage-Specific Gene Loss and Rapid Evolution of a Sperm-Specific Ion Channel Complex: CatSpers and CatSperβ
journal, October 2008
- Cai, Xinjiang; Clapham, David E.
- PLoS ONE, Vol. 3, Issue 10
Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.)
journal, May 2013
- Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath
- PLoS ONE, Vol. 8, Issue 5
Insights into the Development and Evolution of Exaggerated Traits Using De Novo Transcriptomes of Two Species of Horned Scarab Beetles
journal, February 2014
- Warren, Ian A.; Vera, J. Cristobal; Johns, Annika
- PLoS ONE, Vol. 9, Issue 2
PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants
journal, February 2015
- Niroula, Abhishek; Urolagin, Siddhaling; Vihinen, Mauno
- PLOS ONE, Vol. 10, Issue 2
A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis
journal, August 2017
- Zhao, Pengshan; Wang, Lirong; Zhao, Xin
- PLOS ONE, Vol. 12, Issue 8
Molecular identification of the phosphate transporter family 1 (PHT1) genes and their expression profiles in response to phosphorus deprivation and other abiotic stresses in Brassica napus
journal, July 2019
- Li, Yu; Wang, Xue; Zhang, Hao
- PLOS ONE, Vol. 14, Issue 7
Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)
journal, September 2019
- Maheshwari, P.; Kummari, Divya; Palakolanu, Sudhakar Reddy
- PLOS ONE, Vol. 14, Issue 9
The discovery of Halictivirus resolves the Sinaivirus phylogeny.
text, January 2017
- Bigot, Diane; Dalmon, Anne; Roy, Bronwen
- Apollo - University of Cambridge Repository
An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians
journal, June 2016
- Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko
- Frontiers in Chemistry, Vol. 4
Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)
journal, November 2016
- Cao, Yunpeng; Han, Yahui; Jin, Qing
- Frontiers in Plant Science, Vol. 7
Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica
journal, November 2017
- Teng, Linhong; Han, Wentao; Fan, Xiao
- Frontiers in Plant Science, Vol. 8
The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection
journal, December 2019
- Zu, Qian-Li; Qu, Yan-Ying; Ni, Zhi-Yong
- Genes, Vol. 10, Issue 12
Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea
journal, October 2018
- Liu, Tingting; Yu, Hui; Xiong, Xingpeng
- International Journal of Molecular Sciences, Vol. 19, Issue 11
Hadrurid Scorpion Toxins: Evolutionary Conservation and Selective Pressures
journal, November 2019
- Santibáñez-López, Carlos E.; Graham, Matthew R.; Sharma, Prashant P.
- Toxins, Vol. 11, Issue 11
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
journal, October 2015
- Nguyen, Marcus; Ekstrom, Alex; Li, Xueqiong
- Toxins, Vol. 7, Issue 10
Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)
journal, October 2016
- McKain, Michael R.; McNeal, Joel R.; Kellar, P. Roxanne
- American Journal of Botany, Vol. 103, Issue 10
Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome
journal, January 2018
- Lamm, Katherine Young Bezold; Johnson, Maddison L.; Baker Phillips, Julie
- eLife, Vol. 7