Natural Allelic Variations in Highly Polyploidy Saccharum Complex

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

doi:10.3389/fpls.2016.00804

Title: Natural Allelic Variations in Highly Polyploidy Saccharum Complex

Journal Article · Wed Jun 08 00:00:00 EDT 2016 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2016.00804· OSTI ID:1379186

Song, Jian ^[1]; Yang, Xiping ^[2]; Resende, Jr., Marcio F. R. ^[3]; Neves, Leandro G. ^[3]; Todd, James ^[4]; Zhang, Jisen ^[5]; Comstock, Jack C. ^[6]; Wang, Jianping ^[7]

Univ. of Florida, Gainesville, FL (United States); Dezhou Univ., Dezhou (China)
Univ. of Florida, Gainesville, FL (United States)
RAPiD Genomics LLC, Gainesville, FL (United States)
United States Dept. of Agriculture-Agricultural Research Service, Houma, LA (United States); United States Dept. of Agriculture-Agricultural Research Service, Canal Point, FL (United States)
Fujian Agriculture and Forestry Univ., Fuzhou (China)
United States Dept. of Agriculture-Agricultural Research Service, Canal Point, FL (United States)
Univ. of Florida, Gainesville, FL (United States); Fujian Agriculture and Forestry Univ., Fuzhou (China)

Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

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Research Organization:: Univ. of Florida, Gainesville, FL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 1379186

Journal Information:: Frontiers in Plant Science, Vol. 7; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 28 works

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References (84)

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases Garcia, A. A. F.; Kido, E. A.; Meza, A. N. Theoretical and Applied Genetics, Vol. 112, Issue 2 https://doi.org/10.1007/s00122-005-0129-6	journal	November 2005
The Sorghum bicolor genome and the diversification of grasses Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy Nature, Vol. 457, Issue 7229 https://doi.org/10.1038/nature07723	journal	January 2009
Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) Zheng, Lei-Ying; Guo, Xiao-Sen; He, Bing Genome Biology, Vol. 12, Issue 11 https://doi.org/10.1186/gb-2011-12-11-r114	journal	January 2011
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data Aguiar, Derek; Istrail, Sorin Journal of Computational Biology, Vol. 19, Issue 6 https://doi.org/10.1089/cmb.2012.0084	journal	June 2012
A new interspecific, Gossypium hirsutum × G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton Lacape, Jean-Marc; Jacobs, J.; Arioli, T. Theoretical and Applied Genetics, Vol. 119, Issue 2 https://doi.org/10.1007/s00122-009-1037-y	journal	April 2009
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0090581	journal	March 2014
Building the sugarcane genome for biotechnology and identifying evolutionary trends de Setta, Nathalia; Monteiro-Vitorello, Cláudia; Metcalfe, Cushla BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-540	journal	January 2014
ClustalW-MPI: ClustalW analysis using distributed and parallel computing Li, K. -B. Bioinformatics, Vol. 19, Issue 12 https://doi.org/10.1093/bioinformatics/btg192	journal	August 2003
Genome size variation in three Saccharum species Zhang, Jisen; Nagai, Chifumi; Yu, Qingyi Euphytica, Vol. 185, Issue 3 https://doi.org/10.1007/s10681-012-0664-6	journal	March 2012
Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs Woodhouse, Margaret R.; Schnable, James C.; Pedersen, Brent S. PLoS Biology, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pbio.1000409	journal	June 2010
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum Grativol, Clícia; Regulski, Michael; Bertalan, Marcelo The Plant Journal, Vol. 79, Issue 1 https://doi.org/10.1111/tpj.12539	journal	June 2014
Dindel: Accurate indel calls from short-read data Albers, C. A.; Lunter, G.; MacArthur, D. G. Genome Research, Vol. 21, Issue 6 https://doi.org/10.1101/gr.112326.110	journal	October 2010
A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers Kriegner, Albert; Cervantes, Jim Carlos; Burg, Kornel Molecular Breeding, Vol. 11, Issue 3, p. 169-185 https://doi.org/10.1023/A:1022870917230	journal	January 2003
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers Andru, Suman; Pan, Yong-Bao; Thongthawee, Songkran Theoretical and Applied Genetics, Vol. 123, Issue 1 https://doi.org/10.1007/s00122-011-1568-x	journal	April 2011
Next-generation sequencing technologies and their implications for crop genetics and breeding Varshney, Rajeev K.; Nayak, Spurthi N.; May, Gregory D. Trends in Biotechnology, Vol. 27, Issue 9 https://doi.org/10.1016/j.tibtech.2009.05.006	journal	September 2009
UNAFold Markham, Nicholas R.; Zuker, Michael Bioinformatics https://doi.org/10.1007/978-1-60327-429-6_1	book	January 2008
Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene Raboin, L. -M.; Oliveira, K. M.; Lecunff, L. Theoretical and Applied Genetics, Vol. 112, Issue 7 https://doi.org/10.1007/s00122-006-0240-3	journal	March 2006
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland Furtwängler, Anja; Rohrlach, A. B.; Lamnidis, Thiseas C. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15560-x	journal	April 2020
Targeted introduction of heritable point mutations into the plant mitochondrial genome Forner, Joachim; Kleinschmidt, Dennis; Meyer, Etienne H. Nature Plants, Vol. 8, Issue 3 https://doi.org/10.1038/s41477-022-01108-y	journal	March 2022
Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes D'Hont, Angélique; Ison, David; Alix, Karine Genome, Vol. 41, Issue 2 https://doi.org/10.1139/g98-023	journal	April 1998
Relative Importance for Linear Regression in R : The Package relaimpo Grömping, Ulrike Journal of Statistical Software, Vol. 17, Issue 1 https://doi.org/10.18637/jss.v017.i01	journal	January 2006
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge Brownstein, Catherine A.; Beggs, Alan H.; Homer, Nils Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r53	journal	January 2014
Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations Clevenger, Josh; Chavarro, Carolina; Pearl, Stephanie A. Molecular Plant, Vol. 8, Issue 6 https://doi.org/10.1016/j.molp.2015.02.002	journal	June 2015
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
Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes Wang, Jianping; Roe, Bruce; Macmil, Simone BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-261	journal	January 2010
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem Lippert, R. Briefings in Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1093/bib/3.1.23	journal	January 2002
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
agriGO: a GO analysis toolkit for the agricultural community Du, Zhou; Zhou, Xin; Ling, Yi Nucleic Acids Research, Vol. 38, Issue suppl_2 https://doi.org/10.1093/nar/gkq310	journal	April 2010
Fast and accurate long-read alignment with Burrows–Wheeler transform Li, Heng; Durbin, Richard Bioinformatics, Vol. 26, Issue 5 https://doi.org/10.1093/bioinformatics/btp698	journal	January 2010
Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content Springer, Nathan M.; Ying, Kai; Fu, Yan PLoS Genetics, Vol. 5, Issue 11 https://doi.org/10.1371/journal.pgen.1000734	journal	November 2009
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
Evaluating oligonucleotide properties for DNA microarray probe design Xia, Xiao-Qin; Jia, Zhenyu; Porwollik, Steffen Nucleic Acids Research, Vol. 38, Issue 11 https://doi.org/10.1093/nar/gkq039	journal	March 2010
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
Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes Sugimoto, N.; Nakano, S. -i.; Yoneyama, M. Nucleic Acids Research, Vol. 24, Issue 22 https://doi.org/10.1093/nar/24.22.4501	journal	November 1996
Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction Nayak, Spurthi N.; Song, Jian; Villa, Andrea PLoS ONE, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pone.0110856	journal	October 2014
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
MELTING, computing the melting temperature of nucleic acid duplex Le Novere, N. Bioinformatics, Vol. 17, Issue 12 https://doi.org/10.1093/bioinformatics/17.12.1226	journal	December 2001
Haplotype analysis of sucrose synthase gene family in three Saccharum species Zhang, Jisen; Arro, Jie; Chen, Youqiang BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-314	journal	January 2013
Phenotypic characterization of the Miami World Collection of sugarcane (Saccharum spp.) and related grasses for selecting a representative core Todd, James; Wang, Jianping; Glaz, Barry Genetic Resources and Crop Evolution, Vol. 61, Issue 8 https://doi.org/10.1007/s10722-014-0132-3	journal	June 2014
Targeted re-sequencing of the allohexaploid wheat exome: Wheat exome capture and targeted re-sequencing Winfield, Mark O.; Wilkinson, Paul A.; Allen, Alexandra M. Plant Biotechnology Journal, Vol. 10, Issue 6 https://doi.org/10.1111/j.1467-7652.2012.00713.x	journal	June 2012
Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes D'Hont, Angélique; Ison, David; Alix, Karine Genome, Vol. 41, Issue 2 https://doi.org/10.1139/gen-41-2-221	journal	January 1998
Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples Li, Heng arXiv https://doi.org/10.48550/arxiv.1404.0929	text	January 2014
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes Jordan, Katherine W.; Wang, Shichen; Lun, Yanni Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0606-4	journal	February 2015
Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant: Targeted enrichment of sugarcane DNA Bundock, Peter C.; Casu, Rosanne E.; Henry, Robert J. Plant Biotechnology Journal, Vol. 10, Issue 6 https://doi.org/10.1111/j.1467-7652.2012.00707.x	journal	May 2012
Selfing rate estimation in sugarcane under unfavorable natural conditions of crossing by using microsatellite markers Melloni, M. L. G.; Scarpari, M. S.; Pinto, L. R. Genetics and Molecular Research, Vol. 13, Issue 1 https://doi.org/10.4238/2014.March.31.8	journal	January 2014
Linkage disequilibrium among modern sugarcane cultivars Jannoo, N.; Grivet, L.; Dookun, A. Theoretical and Applied Genetics, Vol. 99, Issue 6 https://doi.org/10.1007/s001220051414	journal	October 1999
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome Saintenac, Cyrille; Jiang, Dayou; Akhunov, Eduard D. Genome Biology, Vol. 12, Issue 9 https://doi.org/10.1186/gb-2011-12-9-r88	journal	January 2011
The Sorghum bicolor genome and the diversification of grasses H., Paterson, A.; E., Bowers, J.; R., Bruggmann, Nature Publishing Group https://doi.org/10.5167/uzh-16962	text	January 2009
The evolution of gene duplications: classifying and distinguishing between models Innan, Hideki; Kondrashov, Fyodor Nature Reviews Genetics, Vol. 11, Issue 2 https://doi.org/10.1038/nrg2689	journal	January 2010
PAML 4: Phylogenetic Analysis by Maximum Likelihood Yang, Z. Molecular Biology and Evolution, Vol. 24, Issue 8 https://doi.org/10.1093/molbev/msm088	journal	April 2007
Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Gaut, B. S.; Morton, B. R.; McCaig, B. C. Proceedings of the National Academy of Sciences, Vol. 93, Issue 19 https://doi.org/10.1073/pnas.93.19.10274	journal	September 1996
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor Swanson-Wagner, R. A.; Eichten, S. R.; Kumari, S. Genome Research, Vol. 20, Issue 12 https://doi.org/10.1101/gr.109165.110	journal	October 2010
The Biotechnology Roadmap for Sugarcane Improvement Hotta, Carlos T.; Lembke, Carolina G.; Domingues, Douglas S. Tropical Plant Biology, Vol. 3, Issue 2 https://doi.org/10.1007/s12042-010-9050-5	journal	April 2010
An Improved Filtering Algorithm for Big Read Datasets Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand arXiv https://doi.org/10.48550/arxiv.1610.03443	preprint	January 2016
Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane Vettore, A. L. Genome Research, Vol. 13, Issue 12 https://doi.org/10.1101/gr.1532103	journal	December 2003
ggplot2 Wickham, Hadley Springer New York, NY https://doi.org/10.1007/978-0-387-98141-3	book	January 2009
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Auwera, Geraldine A.; Carneiro, Mauricio O.; Hartl, Christopher Current Protocols in Bioinformatics, Vol. 43, Issue 1 https://doi.org/10.1002/0471250953.bi1110s43	journal	October 2013
Structural variations in plant genomes Saxena, R. K.; Edwards, D.; Varshney, R. K. Briefings in Functional Genomics, Vol. 13, Issue 4 https://doi.org/10.1093/bfgp/elu016	journal	June 2014
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis Haas, Brian J.; Papanicolaou, Alexie; Yassour, Moran Nature Protocols, Vol. 8, Issue 8 https://doi.org/10.1038/nprot.2013.084	journal	July 2013
RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. Bonierbale, M. W.; Plaisted, R. L.; Tanksley, S. D. Genetics, Vol. 120, Issue 4 https://doi.org/10.1093/genetics/120.4.1095	journal	December 1988
Resorcinol Hydroxylase of Azoarcus anaerobius: Molybdenum Dependence, Activity, and Heterologous Expression Darley, Paula I.; Hellstern, Jutta; Schink, Bernhard Current Microbiology, Vol. 77, Issue 11 https://doi.org/10.1007/s00284-020-02186-x	journal	September 2020
Whole-exome targeted sequencing of the uncharacterized pine genome Neves, Leandro G.; Davis, John M.; Barbazuk, William B. The Plant Journal, Vol. 75, Issue 1 https://doi.org/10.1111/tpj.12193	journal	May 2013
Haplotype assembly in polyploid genomes and identical by descent shared tracts Aguiar, Derek; Istrail, Sorin Bioinformatics, Vol. 29, Issue 13 https://doi.org/10.1093/bioinformatics/btt213	journal	June 2013
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing O'Rawe, Jason; Jiang, Tao; Sun, Guangqing Genome Medicine, Vol. 5, Issue 3 https://doi.org/10.1186/gm432	journal	January 2013
Characterization and functional analysis of phytoene synthase gene family in tobacco Wang, Zhaojun; Zhang, Lin; Dong, Chen BMC Plant Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s12870-020-02816-3	journal	January 2021
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis Mandal, Malay; Okoreeh, Michael K.; Kennedy, Domenick E. Nature Immunology, Vol. 20, Issue 10 https://doi.org/10.1038/s41590-019-0468-0	journal	September 2019
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202. Article published online before March 2002	journal	March 2002
Toward better understanding of artifacts in variant calling from high-coverage samples Li, Heng Bioinformatics, Vol. 30, Issue 20 https://doi.org/10.1093/bioinformatics/btu356	journal	June 2014
Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage Aitken, K. S.; Jackson, P. A.; McIntyre, C. L. Genome, Vol. 50, Issue 8 https://doi.org/10.1139/g07-056	journal	August 2007
MOSAIK: A hash-based algorithm for accurate next-generation sequencing read mapping Lee, Wan-Ping; Stromberg, Michael; Ward, Alistair arXiv https://doi.org/10.48550/arxiv.1309.1149	text	January 2013
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
BEDTools: a flexible suite of utilities for comparing genomic features Quinlan, Aaron R.; Hall, Ira M. Bioinformatics, Vol. 26, Issue 6 https://doi.org/10.1093/bioinformatics/btq033	journal	January 2010
Analysis of genetic diversity in the bioenergy plant Erianthus arundinaceus (Poaceae: Andropogoneae) using amplified fragment length polymorphism markers Tsuruta, Shin-ichi; Ebina, Masumi; Kobayashi, Makoto Grassland Science, Vol. 58, Issue 3 https://doi.org/10.1111/j.1744-697X.2012.00258.x	journal	July 2012
Repeat subtraction-mediated sequence capture from a complex genome: Sequence capture in maize Fu, Yan; Springer, Nathan M.; Gerhardt, Daniel J. The Plant Journal, Vol. 62, Issue 5 https://doi.org/10.1111/j.1365-313X.2010.04196.x	journal	March 2010
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W. Nature Genetics, Vol. 53, Issue 3 https://doi.org/10.1038/s41588-021-00778-2	journal	March 2021
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data McKenna, A.; Hanna, M.; Banks, E. Genome Research, Vol. 20, Issue 9 https://doi.org/10.1101/gr.107524.110	journal	July 2010
Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae Al-Janabi, S. M.; McClelland, M.; Petersen, C. Theoretical and Applied Genetics, Vol. 88, Issue 8 https://doi.org/10.1007/bf00220799	journal	September 1994
GMAP: a genomic mapping and alignment program for mRNA and EST sequences Wu, T. D.; Watanabe, C. K. Bioinformatics, Vol. 21, Issue 9 https://doi.org/10.1093/bioinformatics/bti310	journal	February 2005
Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells Zhao, Ruifeng; Zuo, Qisheng; Yuan, Xia Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23242-5	journal	May 2021
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
Accumulation of DNA damage alters microRNA gene transcription in Arabidopsis thaliana Du, Juan; Liu, Yang; Lu, Lu BMC Plant Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s12870-022-03951-9	journal	December 2022
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w Cingolani, Pablo; Platts, Adrian; Wang, Le Lily Fly, Vol. 6, Issue 2 https://doi.org/10.4161/fly.19695	journal	April 2012

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60 APPLIED LIFE SCIENCES
59 BASIC BIOLOGICAL SCIENCES
Saccharum complex
sugarcane
target enrichment sequencing
polyploid
allelic variations
SNP(s)

Title: Natural Allelic Variations in Highly Polyploidy Saccharum Complex

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