The complex polyploid genome architecture of sugarcane

Healey, A. L.; Garsmeur, O.; Lovell, J. T.; Shengquiang, S.; Sreedasyam, A.; Jenkins, J.; Plott, C. B.; Piperidis, N.; Pompidor, N.; Llaca, V.; Metcalfe, C. J.; Doležel, J.; Cápal, P.; Carlson, J. W.; Hoarau, J. Y.; Hervouet, C.; Zini, C.; Dievart, A.; Lipzen, A.; Williams, M.; Boston, L. B.; Webber, J.; Keymanesh, K.; Tejomurthula, S.; Rajasekar, S.; Suchecki, R.; Furtado, A.; May, G.; Parakkal, P.; Simmons, B. A.; Barry, K.; Henry, R. J.; Grimwood, J.; Aitken, K. S.; Schmutz, J.; D’Hont, A.

doi:10.1038/s41586-024-07231-4

Title: The complex polyploid genome architecture of sugarcane

Journal Article · 27 March 2024 · Nature (London)

DOI: https://doi.org/10.1038/s41586-024-07231-4 · OSTI ID:2426887

^[1]; Garsmeur, O. ^[2];

^[3];

^[4];

^[1];

^[5]; Pompidor, N. ^[2];

^[6];

^[7];

^[8]; Cápal, P. ^[8]; Carlson, J. W. ^[4];

^[9];

^[2]; Zini, C. ^[2];

^[2]; Lipzen, A. ^[4]; Williams, M. ^[1] more »

HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
French Agricultural Research Centre for International Development (CIRAD) (France); Montpellier Univ. (France)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sugar Research Australia (Australia)
Corteva Agriscience, Johnston, IA (United States)
Commonwealth Scientific and Industrial Research Organisation (CSIRO) (Australia)
Czech Academy of Sciences (CAS) (Czech Republic)
French Agricultural Research Centre for International Development (CIRAD) (France); Montpellier Univ. (France); eRcane Research Centre (France)
Univ. of Arizona, Tucson, AZ (United States)
Univ. of Queensland, Brisbane, QLD (Australia)
Univ. of Queensland, Brisbane, QLD (Australia); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Joint Genome Institute (JGI); USDOE Joint Genome Institute (JGI)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2426887

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 8009 Vol. 628; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (78)

BEDTools: The Swiss-Army Tool for Genome Feature Analysis: BEDTools: the Swiss-Army Tool for Genome Feature Analysis Quinlan, Aaron R. Current Protocols in Bioinformatics, Vol. 47, Issue 1 https://doi.org/10.1002/0471250953.bi1112s47	journal	September 2014
Problems in breeding and cytology of sugar cane Bremer, G. Euphytica, Vol. 10, Issue 1 https://doi.org/10.1007/BF00037206	journal	March 1961
A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’ Daugrois, J. H.; Grivet, L.; Roques, D. Theoretical and Applied Genetics, Vol. 92, Issue 8 https://doi.org/10.1007/BF00224049	journal	June 1996
Molecular dissection of complex traits in autopolyploids: mapping QTLs affecting sugar yield and related traits in sugarcane Ming, R.; Wang, Y.; Draye, X. Theoretical and Applied Genetics, Vol. 105, Issue 2 https://doi.org/10.1007/s00122-001-0861-5	journal	August 2002
Genetic dissection of a modern sugarcane cultivar (Saccharum spp.).II. Detection of QTLs for yield components Hoarau, J. -Y.; Grivet, L.; Offmann, B. Theoretical and Applied Genetics, Vol. 105, Issue 6 https://doi.org/10.1007/s00122-002-1047-5	journal	November 2002
A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar Aitken, K. S.; Jackson, P. A.; McIntyre, C. L. Theoretical and Applied Genetics, Vol. 110, Issue 5 https://doi.org/10.1007/s00122-004-1813-7	journal	February 2005
Quantitative trait loci identified for sugar related traits in a sugarcane (Saccharum spp.) cultivar × Saccharum officinarum population Aitken, K. S.; Jackson, P. A.; McIntyre, C. L. Theoretical and Applied Genetics, Vol. 112, Issue 7 https://doi.org/10.1007/s00122-006-0233-2	journal	March 2006
Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars Costet, L.; Le Cunff, L.; Royaert, S. Theoretical and Applied Genetics, Vol. 125, Issue 5 https://doi.org/10.1007/s00122-012-1875-x	journal	May 2012
Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification Metcalfe, Cushla J.; Li, Jingchuan; Zheng, Bangyou Theoretical and Applied Genetics, Vol. 135, Issue 4 https://doi.org/10.1007/s00122-022-04030-1	journal	March 2022
Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers Hoarau, J. -Y.; Offmann, B.; D’Hont, A. Theoretical and Applied Genetics, Vol. 103, Issue 1 https://doi.org/10.1007/s001220000390	journal	July 2001
Application of synteny across Poaceae to determine the map location of a sugarcane rust resistance gene Asnaghi, C.; Paulet, F.; Kaye, C. Theoretical and Applied Genetics, Vol. 101, Issue 5-6 https://doi.org/10.1007/s001220051568	journal	October 2000
Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars Huang, Yongji; Chen, Hong; Han, Jinlei Chromosoma, Vol. 129, Issue 1 https://doi.org/10.1007/s00412-019-00729-1	journal	December 2019
Physiological roles of plant glycoside hydrolases Minic, Zoran Planta, Vol. 227, Issue 4 https://doi.org/10.1007/s00425-007-0668-y	journal	November 2007
Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane Piperidis, George; Piperidis, Nathalie; D’Hont, Angélique Molecular Genetics and Genomics, Vol. 284, Issue 1 https://doi.org/10.1007/s00438-010-0546-3	journal	June 2010
Characterisation of the double genome structure of modern sugarcane cultivars ( D’Hont, Angélique; Grivet, Laurent; Feldmann, Philippe MGG Molecular & General Genetics, Vol. 250, Issue 4 https://doi.org/10.1007/s004380050092	journal	January 1996
A short review on sugarcane: its domestication, molecular manipulations and future perspectives Dinesh Babu, Kandhalu Sagadevan; Janakiraman, Vardhana; Palaniswamy, Harunipriya Genetic Resources and Crop Evolution, Vol. 69, Issue 8 https://doi.org/10.1007/s10722-022-01430-6	journal	September 2022
Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations Piperidis, Nathalie; Jackson, Phillip A.; D’Hont, Angelique Molecular Breeding, Vol. 21, Issue 2 https://doi.org/10.1007/s11032-007-9124-8	journal	September 2007
Sugarcane Breeding in Reunion: Challenges, Achievements and Future Prospects Dumont, Thomas; Barau, Laurent; Thong-Chane, Audrey Sugar Tech, Vol. 24, Issue 1 https://doi.org/10.1007/s12355-021-00998-0	journal	May 2021
Modification of polysaccharides and plant cell wall by endo-1,4-β-glucanase and cellulose-binding domains Levy, Ilan; Shani, Ziv; Shoseyov, Oded Biomolecular Engineering, Vol. 19, Issue 1 https://doi.org/10.1016/S1389-0344(02)00007-2	journal	June 2002
Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement Liu, Bao; Xu, Chunming; Zhao, Na Journal of Genetics and Genomics, Vol. 36, Issue 9 https://doi.org/10.1016/S1673-8527(08)60143-5	journal	September 2009
Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae) Huang, Chi-Chun; Hung, Kuo-Hsiang; Wang, Wei-Kuang Gene, Vol. 499, Issue 1 https://doi.org/10.1016/j.gene.2012.02.037	journal	May 2012
Flow cytometric chromosome sorting in plants: The next generation Vrána, Jan; Šimková, Hana; Kubaláková, Marie Methods, Vol. 57, Issue 3 https://doi.org/10.1016/j.ymeth.2012.03.006	journal	July 2012
A mosaic monoploid reference sequence for the highly complex genome of sugarcane Garsmeur, Olivier; Droc, Gaetan; Antonise, Rudie Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05051-5	journal	July 2018
Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family Klymiuk, Valentina; Yaniv, Elitsur; Huang, Lin Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06138-9	journal	October 2018
The genomic landscape of molecular responses to natural drought stress in Panicum hallii Lovell, John T.; Jenkins, Jerry; Lowry, David B. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07669-x	journal	December 2018
The mosaic oat genome gives insights into a uniquely healthy cereal crop Kamal, Nadia; Tsardakas Renhuldt, Nikos; Bentzer, Johan Nature, Vol. 606, Issue 7912 https://doi.org/10.1038/s41586-022-04732-y	journal	May 2022
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci Mamidi, Sujan; Healey, Adam; Huang, Pu Nature Biotechnology, Vol. 38, Issue 10 https://doi.org/10.1038/s41587-020-0681-2	journal	October 2020
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Zhang, Jisen; Zhang, Xingtan; Tang, Haibao Nature Genetics, Vol. 50, Issue 11 https://doi.org/10.1038/s41588-018-0237-2	journal	October 2018
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar Sun, Hequan; Jiao, Wen-Biao; Krause, Kristin Nature Genetics, Vol. 54, Issue 3 https://doi.org/10.1038/s41588-022-01015-0	journal	March 2022
Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum Zhang, Qing; Qi, Yiying; Pan, Haoran Nature Genetics, Vol. 54, Issue 6 https://doi.org/10.1038/s41588-022-01084-1	journal	June 2022
Long-read sequence and assembly of segmental duplications Vollger, Mitchell R.; Dishuck, Philip C.; Sorensen, Melanie Nature Methods, Vol. 16, Issue 1 https://doi.org/10.1038/s41592-018-0236-3	journal	December 2018
Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivars Metcalfe, Cushla J.; Li, Jingchuan; Giorgi, Debora Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55652-3	journal	December 2019
A draft chromosome-scale genome assembly of a commercial sugarcane Shearman, Jeremy R.; Pootakham, Wirulda; Sonthirod, Chutima Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-24823-0	journal	November 2022
Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers Jannoo, N.; Grivet, L.; David, J. Heredity, Vol. 93, Issue 5 https://doi.org/10.1038/sj.hdy.6800524	journal	August 2004
The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases Brueggeman, R.; Rostoks, N.; Kudrna, D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 14 https://doi.org/10.1073/pnas.142284999	journal	June 2002
Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Song, K.; Lu, P.; Tang, K. Proceedings of the National Academy of Sciences, Vol. 92, Issue 17 https://doi.org/10.1073/pnas.92.17.7719	journal	August 1995
Three founding ancestral genomes involved in the origin of sugarcane Pompidor, Nicolas; Charron, Carine; Hervouet, Catherine Annals of Botany, Vol. 127, Issue 6 https://doi.org/10.1093/aob/mcab008	journal	February 2021
ggmsa: a visual exploration tool for multiple sequence alignment and associated data Zhou, Lang; Feng, Tingze; Xu, Shuangbin Briefings in Bioinformatics, Vol. 23, Issue 4 https://doi.org/10.1093/bib/bbac222	journal	June 2022
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
Fast and SNP-tolerant detection of complex variants and splicing in short reads Wu, T. D.; Nacu, S. Bioinformatics, Vol. 26, Issue 7, p. 873-881 https://doi.org/10.1093/bioinformatics/btq057	journal	February 2010
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
Minimap2: pairwise alignment for nucleotide sequences Li, Heng Bioinformatics, Vol. 34, Issue 18 https://doi.org/10.1093/bioinformatics/bty191	journal	May 2018
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop Souza, Glaucia Mendes; Van Sluys, Marie-Anne; Lembke, Carolina Gimiliani GigaScience, Vol. 8, Issue 12 https://doi.org/10.1093/gigascience/giz129	journal	November 2019
Genome remodelling in three modern S. officinarumxS. spontaneum sugarcane cultivars Cuadrado, A. Journal of Experimental Botany, Vol. 55, Issue 398 https://doi.org/10.1093/jxb/erh093	journal	March 2004
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
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
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
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
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
Tandem Protein Kinases Emerge as New Regulators of Plant Immunity Klymiuk, Valentyna; Coaker, Gitta; Fahima, Tzion Molecular Plant-Microbe Interactions®, Vol. 34, Issue 10 https://doi.org/10.1094/MPMI-03-21-0073-CR	journal	October 2021
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 NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire Steuernagel, Burkhard; Witek, Kamil; Krattinger, Simon G. Plant Physiology, Vol. 183, Issue 2 https://doi.org/10.1104/pp.19.01273	journal	March 2020
Meiotic abnormalities in sugarcane (Saccharum spp.) and parental species: Evidence for peri‐ and paracentric inversions Oliveira, Gleicy Kelly; Soares, Nina Reis; Costa, Zirlane Portugal Annals of Applied Biology, Vol. 183, Issue 3 https://doi.org/10.1111/aab.12855	journal	August 2023
Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome: Genomic stability in the highly polyploid sugarcane Jannoo, Nazeema; Grivet, Laurent; Chantret, Nathalie The Plant Journal, Vol. 50, Issue 4 https://doi.org/10.1111/j.1365-313X.2007.03082.x	journal	April 2007
The RLK/Pelle family of kinases Gish, Lindsey A.; Clark, Steven E. The Plant Journal, Vol. 66, Issue 1 https://doi.org/10.1111/j.1365-313X.2011.04518.x	journal	March 2011
High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane Garsmeur, Olivier; Charron, Carine; Bocs, Stéphanie New Phytologist, Vol. 189, Issue 2 https://doi.org/10.1111/j.1469-8137.2010.03497.x	journal	October 2010
Distribution and frequency of Bru1, a major brown rust resistance gene, in the sugarcane world collection Parco, Arnold S.; Hale, Anna L.; Avellaneda, Mavir C. Plant Breeding, Vol. 136, Issue 5 https://doi.org/10.1111/pbr.12508	journal	July 2017
The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization McCormick, Ryan F.; Truong, Sandra K.; Sreedasyam, Avinash The Plant Journal, Vol. 93, Issue 2 https://doi.org/10.1111/tpj.13781	journal	December 2017
Sugarcane genome architecture decrypted with chromosome‐specific oligo probes Piperidis, Nathalie; D’Hont, Angélique The Plant Journal, Vol. 103, Issue 6 https://doi.org/10.1111/tpj.14881	journal	July 2020
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes Hufford, Matthew B.; Seetharam, Arun S.; Woodhouse, Margaret R. Science, Vol. 373, Issue 6555 https://doi.org/10.1126/science.abg5289	journal	August 2021
The complete sequence of a human genome Nurk, Sergey; Koren, Sergey; Rhie, Arang Science, Vol. 376, Issue 6588 https://doi.org/10.1126/science.abj6987	journal	April 2022
Evolutionary-scale prediction of atomic-level protein structure with a language model Lin, Zeming; Akin, Halil; Rao, Roshan Science, Vol. 379, Issue 6637 https://doi.org/10.1126/science.ade2574	journal	March 2023
Automated generation of heuristics for biological sequence comparison Slater, Guy St C.; Birney, Ewan BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-31	journal	February 2005
A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers Aitken, Karen S.; McNeil, Meredith D.; Hermann, Scott BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-152	journal	January 2014
pblat: a multithread blat algorithm speeding up aligning sequences to genomes Wang, Meng; Kong, Lei BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-2597-8	journal	January 2019
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism Cooper, Elizabeth A.; Brenton, Zachary W.; Flinn, Barry S. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5734-x	journal	May 2019
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
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies Goel, Manish; Sun, Hequan; Jiao, Wen-Biao Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1911-0	journal	December 2019
Diploid/Polyploid Syntenic Shuttle Mapping and Haplotype-Specific Chromosome Walking Toward a Rust Resistance Gene ( Bru1 ) in Highly Polyploid Sugarcane (2 n ∼ 12 x ∼ 115) Le Cunff, Loïc; Garsmeur, Olivier; Raboin, Louis Marie Genetics, Vol. 180, Issue 1 https://doi.org/10.1534/genetics.108.091355	journal	August 2008
Chromosome Transmission and Meiotic Stability of Sugarcane (Saccharum spp.) Hybrid Derivatives Burner, David M.; Legendre, Benjamin L. Crop Science, Vol. 33, Issue 3 https://doi.org/10.2135/cropsci1993.0011183X003300030036x	journal	May 1993
Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations Vieira, Maria Lucia C.; Almeida, Carmelice B.; Oliveira, Carlos A. Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00213	journal	June 2018
Accelerating Genetic Gain in Sugarcane Breeding Using Genomic Selection Yadav, Seema; Jackson, Phillip; Wei, Xianming Agronomy, Vol. 10, Issue 4 https://doi.org/10.3390/agronomy10040585	journal	April 2020
The rise of the undead Lewis, Jennifer D.; Lo, Timothy; Bastedo, Patrick Plant Signaling & Behavior, Vol. 9, Issue 1 https://doi.org/10.4161/psb.27563	journal	January 2014
Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids Lu, X.; Zhou, H.; Pan, Y. -B. Genetics and Molecular Research, Vol. 14, Issue 4 https://doi.org/10.4238/2015.December.23.26	journal	January 2015
Supplemental Data for: The complex polyploid genome architecture of sugarcane Healey, Adam; Lovell, John T.; Sreedasyam, Avinash figshare https://doi.org/10.6084/m9.figshare.22138004.v1	dataset	January 2024
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism Cooper, Elizabeth; Brenton, Zachary; Flinn, Barry Figshare https://doi.org/10.6084/m9.figshare.c.4519544.v1	collection	January 2019
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies Goel, Manish; Sun, Hequan; Jiao, Wen-Biao figshare https://doi.org/10.6084/m9.figshare.c.4784301.v1	collection	January 2019
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes Lovell, John T.; Sreedasyam, Avinash; Schranz, M. Eric eLife, Vol. 11 https://doi.org/10.7554/eLife.78526	journal	September 2022

Similar Records

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum

Journal Article · 2016 · BMC Genomics · OSTI ID:1287172

Zhang, Jisen; Sharma, Anupma; Yu, Qingyi; +6 more

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Journal Article · 2018 · Nature Communications · OSTI ID:1543745

Garsmeur, Olivier; Droc, Gaetan; Antonise, Rudie; +25 more

The genomic footprints of wild Saccharum species trace domestication, diversification, and modern breeding of sugarcane

Journal Article · 2025 · Cell · OSTI ID:3012831

Garsmeur, Olivier; Rio, Simon; Pompidor, Nicolas; +19 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
agriculture
genome evolution
genome informatics
plant genetics
polyploidy in plants

Title: The complex polyploid genome architecture of sugarcane

Citation Formats

References (78)

Linked Research (1)

Similar Records

Related Subjects