Freeling M, Scanlon MJ, Fowler JE. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr Opin Genet Dev. 2015;35:110–8. https://doi.org/10.1016/j.gde.2015.11.002.
Article
CAS
PubMed
Google Scholar
Soltis PS, Soltis DE. Ancient WGD events as drivers of key innovations in angiosperms. Curr Opin Plant Biol. 2016;30:159–65. https://doi.org/10.1016/j.pbi.2016.03.015.
Article
PubMed
Google Scholar
Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, et al. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. New Phytol. 2015;207(2):454–67. https://doi.org/10.1111/nph.13491.
Article
PubMed
Google Scholar
Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017;18(7):411–24. https://doi.org/10.1038/nrg.2017.26.
Article
CAS
PubMed
Google Scholar
Zhang K, Wang XW, Cheng F. Plant polyploidy: origin, evolution, and its influence on crop domestication. Horticultural Plant J. 2019;5:231–9.
Article
Google Scholar
Cheng F, Wu J, Cai X, Liang J, Freeling M, Wang X. Gene retention, fractionation and subgenome differences in polyploid plants. Nat Plants. 2018;4:258–68.
Article
CAS
PubMed
Google Scholar
Jackson S, Chen ZJ. Genomic and expression plasticity of polyploidy. Curr Opi Plant Biol. 2010;13(2):153–9. https://doi.org/10.1016/j.pbi.2009.11.004.
Article
CAS
Google Scholar
Renny-Byfield S, Gong L, Gallagher JP, Wendel JF. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Mol Biol Evol. 2015;32(4):1063–71. https://doi.org/10.1093/molbev/msv001.
Article
CAS
PubMed
Google Scholar
Cheng F, Sun C, Wu J, Schnable J, Woodhouse MR, Liang JL, et al. Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. New Phytologist. 2016;211:288–99.
Article
CAS
PubMed
Google Scholar
Li AL, Liu DC, Wu J, Zhao XB, Hao M, Geng SF, et al. mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell. 2014;26(5):1878–900. https://doi.org/10.1105/tpc.114.124388.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomas BC, Pedersen B, Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 2006;16(7):934–46. https://doi.org/10.1101/gr.4708406.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang JL, Tian L, Lee HS, Wei NE, Jiang HM, Watson B, et al. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics. 2006;172(1):507–17. https://doi.org/10.1534/genetics.105.047894.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alger EI, Edger PP. One subgenome to rule them all: underlying mechanisms of subgenome dominance. Curr Opin Plant Biol. 2020;54:108–13. https://doi.org/10.1016/j.pbi.2020.03.004.
Article
CAS
PubMed
Google Scholar
Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr Opin Plant Biol. 2012;15:131–9.
Article
CAS
PubMed
Google Scholar
Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan YW, et al. Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Plant Cell. 2017;29(9):2150–67. https://doi.org/10.1105/tpc.17.00010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng F, Wu J, Fang L, Sun SL, Liu B, Lin K, et al. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLos One. 2012;7(5):e36442. https://doi.org/10.1371/journal.pone.0036442.
Pfeifer M, Kugler KG, Sandve SR, Zhan BJ, Rudi H, Hvidsten TR, et al. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014;345(6194):1250091. https://doi.org/10.1126/science.1250091.
Article
CAS
PubMed
Google Scholar
Bird KA, VanBuren R, Puzey JR, Edger PP. The causes and consequences of subgenome dominance in hybrids and recent polyploids. New Phytol. 2018;220(1):87–93. https://doi.org/10.1111/nph.15256.
Article
PubMed
Google Scholar
Chalhoub B, Denoeud F, Liu SY, Parkin IAP, Tang HB, Wang XY, et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345(6199):950–3. https://doi.org/10.1126/science.1253435.
Article
CAS
PubMed
Google Scholar
Levin DA, Soltis DE. Factors promoting polyploid persistence and diversification and limiting diploid speciation during the K-Pg interlude. Curr Opin Plant Biol. 2018;42:1–7. https://doi.org/10.1016/j.pbi.2017.09.010.
Article
PubMed
Google Scholar
Salman-Minkov A, Sabath N, Mayrose I. Whole-genome duplication as a key factor in crop domestication. NatPlants. 2016;2(8). https://doi.org/10.1038/nplants.2016.115.
Vanneste K, Maere S, Van de Peer Y. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc B Biol Sci. 2014;369(1648):20130353. https://doi.org/10.1098/rstb.2013.0353.
Article
Google Scholar
Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants. Science. 2008;320(5875):481–3. https://doi.org/10.1126/science.1153585.
Article
CAS
PubMed
Google Scholar
Cheng F, Sun RF, Hou XL, Zheng HK, Zhang FL, Zhang YY, et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet. 2016;48(10):1218–24. https://doi.org/10.1038/ng.3634.
Article
CAS
PubMed
Google Scholar
Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J. Gene Fractionation and Function in the Ancient Subgenomes of Maize. Mol Biol Evol. 2017;34(8):1825–32. https://doi.org/10.1093/molbev/msx121.
Article
CAS
PubMed
Google Scholar
Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet. 2017;49(4):579–87. https://doi.org/10.1038/ng.3807.
Article
CAS
PubMed
Google Scholar
Liu YC, Du HL, Li PC, Shen YT, Peng H, Liu SL, et al. Pan-Genome of Wild and Cultivated Soybeans. Cell. 2020;182:162.
Article
CAS
PubMed
Google Scholar
Song JM, Guan ZL, Hu JL, Guo CC, Yang ZQ, Wang S, et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants. 2020;6:34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang X, Lee WP, Ye K, Lee C. One reference genome is not enough. Genome Biol. 2019;20(1):104. https://doi.org/10.1186/s13059-019-1717-0.
Article
PubMed
PubMed Central
Google Scholar
Yu JY, Golicz AA, Lu K, Dossa K, Zhang YX, Chen JF, et al. Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. Plant Biotechnol J. 2019;17:881–92.
Article
CAS
PubMed
Google Scholar
Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F, et al. Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Horticulture Res. 2018;5(1):50. https://doi.org/10.1038/s41438-018-0071-9.
Article
CAS
Google Scholar
Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, et al. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020;182:145–61 e123.
Article
CAS
PubMed
PubMed Central
Google Scholar
Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, et al. The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun. 2016;7(1):13390. https://doi.org/10.1038/ncomms13390.
Hubner S, Bercovich N, Todesco M, Mandel JR, Odenheimer J, Ziegler E, et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nat Plants. 2019;5(1):54–62. https://doi.org/10.1038/s41477-018-0329-0.
Article
CAS
PubMed
Google Scholar
Maretty L, Jensen JM, Petersen B, Sibbesen JAN, Liu SY, Villesen P, et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature. 2017;548:87.
Article
CAS
PubMed
Google Scholar
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15(6):589–94. https://doi.org/10.1016/j.gde.2005.09.006.
Article
CAS
PubMed
Google Scholar
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005;102(39):13950–5. https://doi.org/10.1073/pnas.0506758102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao L, Gonda I, Sun HH, Ma QY, Bao K, Tieman DM, et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet. 2019;51:1044.
Article
CAS
PubMed
Google Scholar
Zhao Q, Feng Q, Lu HY, Li Y, Wang A, Tian QL, et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet. 2018;50:279.
Google Scholar
Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun. 2020;11(1):989. https://doi.org/10.1038/s41467-020-14779-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gordon SP, Contreras-Moreira B, Woods DP, Marais DLD, Burgess D, Shu SQ, et al. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun. 2017;8(1):2184. https://doi.org/10.1038/s41467-017-02292-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot. 1935;7:389–452.
Google Scholar
Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SY, et al. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011;43(10):1035–U1157. https://doi.org/10.1038/ng.919.
Article
CAS
PubMed
Google Scholar
Cheng F, Mandakova T, Wu J, Xie Q, Lysak MA, Wang XW. Deciphering the diploid ancestral genome of the mesohexaploid Brassica rapa. Plant Cell. 2013;25(5):1541–54. https://doi.org/10.1105/tpc.113.110486.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lye ZN, Purugganan MD. Copy number variation in domestication. Trends Plant Sci. 2019;24(4):352–65. https://doi.org/10.1016/j.tplants.2019.01.003.
Article
CAS
PubMed
Google Scholar
Wu J, Wei K, Cheng F, Li S, Wang Q, Zhao J, et al. A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa. BMC Plant Biol. 2012;12(1):151. https://doi.org/10.1186/1471-2229-12-151.
Article
CAS
PubMed
PubMed Central
Google Scholar
Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat Plants. 2018;4(11):879–87. https://doi.org/10.1038/s41477-018-0289-4.
Article
CAS
PubMed
Google Scholar
Li PR, Su TB, Zhao XY, Wang WH, Zhang DS, Yu YJ, Bayer PE, Edwards D, Yu SC, Zhang FL. Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. Plant Biotechnol J. 2021. https://doi.org/10.1111/pbi.13522.
Boutte J, Maillet L, Chaussepied T, Letort S, Aury JM, Belser C, et al. Genome size variation and comparative genomics reveal intraspecific diversity in Brassica rapa. Front Plant Sci. 2020;11. https://doi.org/10.3389/fpls.2020.577536.
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356(6333):92–5. https://doi.org/10.1126/science.aal3327.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cai X, Wu J, Liang J, Lin R, Zhang K, Cheng F, et al. Improved Brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes. Theor Appl Genet. 2020;133(11):3187–99. https://doi.org/10.1007/s00122-020-03664-3.
Article
CAS
PubMed
Google Scholar
Sun SL, Zhou YS, Chen J, Shi JP, Zhao HM, Zhao HN, et al. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet. 2018;50:1289.
Article
CAS
PubMed
Google Scholar
Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol. 2006;7(11):847–59. https://doi.org/10.1038/nrm2020.
Article
CAS
PubMed
Google Scholar
Murat F, Louis A, Maumus F, Armero A, Cooke R, Quesneville H, et al. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol. 2015;16(1):262. https://doi.org/10.1186/s13059-015-0814-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng F, Liang JL, Cai CC, Cai X, Wu J, Wang XW. Genome sequencing supports a multi-vertex model for Brassiceae species. Curr Opin Plant Biol. 2017;36:79–87. https://doi.org/10.1016/j.pbi.2017.01.006.
Article
CAS
PubMed
Google Scholar
Liu SY, Liu YM, Yang XH, Tong CB, Edwards D, Parkin IAP, Zhao MX, Ma JX, Yu JY, Huang SM, et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun. 2014;5(3930):3930. https://doi.org/10.1038/ncomms4930.
Perumal S, Koh CS, Jin L, Buchwaldt M, Higgins EE, Zheng C, et al. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nat Plants. 2020;6(8):929–41. https://doi.org/10.1038/s41477-020-0735-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang X, Yue Z, Mei S, Qiu Y, Yang X, Chen X, et al. A de novo genome of a Chinese radish cultivar. Horticultural Plant J. 2015;1:155–64.
Google Scholar
Gao LW, Lyu SW, Tang J, Zhou DY, Bonnema G, Xiao D, et al. Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage. Sci Rep. 2017;7:42229. https://doi.org/10.1038/srep42229.
Schnable JC, Springer NM, Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A. 2011;108(10):4069–74. https://doi.org/10.1073/pnas.1101368108.
Article
PubMed
PubMed Central
Google Scholar
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin DC, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 2012;492:423.
Article
CAS
PubMed
Google Scholar
Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, et al. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Gen. 2018;14(3):e1007267. https://doi.org/10.1371/journal.pgen.1007267.
Article
CAS
Google Scholar
Byrne ME. Networks in leaf development. Curr Opin Plant Biol. 2005;8(1):59–66. https://doi.org/10.1016/j.pbi.2004.11.009.
Article
PubMed
Google Scholar
Husbands AY, Chitwood DH, Plavskin Y, Timmermans MCP. Signals and prepatterns: new insights into organ polarity in plants. Genes Dev. 2009;23(17):1986–97. https://doi.org/10.1101/gad.1819909.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kidner CA, Timmermans MCP. Mixing and matching pathways in leaf polarity. Curr Opin Plant Biol. 2007;10(1):13–20. https://doi.org/10.1016/j.pbi.2006.11.013.
Article
PubMed
Google Scholar
Townsley BT, Sinha NR. A new development: evolving concepts in leaf ontogeny. Ann Rev Plant Biol. 2012;63:535–62.
Article
CAS
Google Scholar
Ge Y, Ramchiary N, Wang T, Liang C, Wang N, Wang Z, et al. Mapping quantitative trait loci for leaf and heading-related traits in chinese cabbage (Brassica rapa L. ssp pekinesis). Horticulture Environ Biotechnol. 2011;52:494–501.
Article
Google Scholar
Inoue T, Kubo N, Kondo T, Hirai M. Detection of quantitative trait loci for heading traits in Brassica rapa using different heading types of Chinese cabbage. J Horticultural Sci Biotechnol. 2015;90(3):311–7. https://doi.org/10.1080/14620316.2015.11513188.
Article
Google Scholar
Allen GC, Flores-Vergara MA, Krasnyanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc. 2006;1:2320–5.
Article
CAS
PubMed
Google Scholar
Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015;12(8):780–6. https://doi.org/10.1038/nmeth.3454.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grob S, Schmid MW, Grossniklaus U. Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Mol Cell. 2014;55:678–93.
Article
CAS
PubMed
Google Scholar
Zimin AV, Puiu D, Luo MC, Zhu TT, Koren S, Marcais G, et al. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res. 2017;27(5):787–92. https://doi.org/10.1101/gr.213405.116.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waterhouse RM, Seppey M, Simao FA, Manni M, Ioannidis P, Klioutchnikov G, et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2018;35:543–8.
Article
CAS
PubMed
Google Scholar
Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3(1):95–8. https://doi.org/10.1016/j.cels.2016.07.002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson JT, Turner D, Durand NC, Thorvaldsdottir H, Mesirov JP, Aiden EL. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst. 2018;6:256.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12. https://doi.org/10.1186/gb-2004-5-2-r12.
Article
PubMed
PubMed Central
Google Scholar
Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019;20(1):275. https://doi.org/10.1186/s13059-019-1905-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2009;Chapter 4(Unit 4):10.
PubMed
Google Scholar
Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005;33(Web Server):W451–4. https://doi.org/10.1093/nar/gki487.
Article
CAS
PubMed
PubMed Central
Google Scholar
Birney E, Clamp M, Durbin R. GeneWise and genomewise. Genome Res. 2004;14(5):988–95. https://doi.org/10.1101/gr.1865504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–U130. https://doi.org/10.1038/nbt.1883.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003;31(19):5654–66. https://doi.org/10.1093/nar/gkg770.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9(1):R7. https://doi.org/10.1186/gb-2008-9-1-r7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37(Database):D211–5. https://doi.org/10.1093/nar/gkn785.
Article
CAS
PubMed
Google Scholar
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238. https://doi.org/10.1186/s13059-019-1832-y.
Article
PubMed
PubMed Central
Google Scholar
Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13:1194–202.
Article
CAS
PubMed
Google Scholar
Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35(Web Server):W265–8. https://doi.org/10.1093/nar/gkm286.
Article
PubMed
PubMed Central
Google Scholar
Ou SJ, Jiang N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. 2018;176(2):1410–22. https://doi.org/10.1104/pp.17.01310.
Article
CAS
PubMed
Google Scholar
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33(2):511–8. https://doi.org/10.1093/nar/gki198.
Article
CAS
PubMed
PubMed Central
Google Scholar
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56(4):564–77. https://doi.org/10.1080/10635150701472164.
Article
CAS
PubMed
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033.
Article
CAS
PubMed
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3. Fly. 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen SF, Zhou YQ, Chen YR. Gu J: fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:884–90.
Article
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. https://doi.org/10.1093/bioinformatics/btp324.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eggertsson HP, Jonsson H, Kristmundsdottir S, Hjartarson E, Kehr B, Masson G, et al. Graphtyper enables population-scale genotyping using pangenome graphs. Nat Genet. 2017;49:1654.
Article
CAS
PubMed
Google Scholar
Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, et al. High-resolution comparative analysis of great ape genomes. Science. 2018;360:1085.
Article
CAS
Google Scholar
Garrison E, Siren J, Novak AM, Hickey G, Eizenga JM, Dawson ET, et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol. 2018;36:875.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goel M, Sun HQ, Jiao WB, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019;20(1):277. https://doi.org/10.1186/s13059-019-1911-0.
Article
PubMed
PubMed Central
Google Scholar
Kim D, Landmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–U121. https://doi.org/10.1038/nmeth.3317.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):278. https://doi.org/10.1186/s13059-019-1910-1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLoS Computat Biol. 2018;14(1):e1005944. https://doi.org/10.1371/journal.pcbi.1005944.
Article
CAS
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094–100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng F, Wu J, Fang L, Wang XW. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci. 2012;3. https://doi.org/10.3389/fpls.2012.00198.
Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 2002;12(12):1805–14. https://doi.org/10.1101/gr.631202.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu X, Liu X, Ge S, Jensen JD, Hu FY, Li X, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol. 2012;30(1):105–U157. https://doi.org/10.1038/nbt.2050.
Article
CAS
Google Scholar
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007;449(7164):913–U912. https://doi.org/10.1038/nature06250.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. https://doi.org/10.1093/bioinformatics/btr330.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cai X, Chang L, Zhang T, Chen H, Zhang L, Lin R, et al. Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Dataset NCBI. 2021; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA730930.
Zhang Z, Zhao WM, Xiao JF, Bao YM, Wang F, Hao LL, et al. Database resources of the BIG Data Center in 2019. Nucleic Acids Res. 2019;47:D8–D14.
Article
CAS
Google Scholar
Cai et al. Genome assemblies and annotations of Brassica rapa accessions. 2021. https://doi.org/10.6084/m9.figshare.14571297.v1.
Google Scholar