7种茄科植物染色体的演化关系研究

doi:10.16420/j.issn.0513-353x.2022-0328

摘要/Abstract

摘要：

为了追溯茄科（Solanaceae）物种染色体的演化关系，对7种茄科物种进行了系统的比较基因组学分析，利用模式植物番茄的基因组为参考模板，全面鉴定7个物种间的基因组共线性关系，以此为基础建立了茄科的基因组片段单元系统，并基于该系统重建了具有12条染色体的祖先基因组，阐明祖先基因组主要通过基因组片段的易位和倒位逐步形成目前的茄科基因组结构，且这些重排事件多发生在着丝粒等重复序列富集的区域。研究结果为深入认识茄科以及其他植物的基因组进化和物种分化等提供理论参考。

关键词: 茄科, 比较基因组, 祖先基因组, 染色体重排, 着丝粒, 重复序列

Abstract:

In order to trace the evolution of chromosomes of Solanaceae species，a systematic comparative genomic analysis was carried out on seven Solanaceae species. Using the genome of model plant tomato as a reference template，the collinear relationship among seven species of Solanaceae were comprehensively identified，and the genome fragment unit system of Solanaceae was established. Based on this system，the ancestral genome of Solanaceae with 12 chromosomes was reconstructed. The results showed that the ancestral genome gradually formed the current genome structure of Solanaceae mainly through translocation and inversion of genome fragments，and these rearrangement events mostly occurred in the regions of centromere and other repeated sequences were enriched. This study provided an important theoretical reference for further understanding the genome evolution and species differentiation of Solanaceae and other plants.

Key words: Solanaceae, comparative genome, ancestral genome, chromosome rearrangement, centromere, repeat sequence

中图分类号:

S641

付钰, 张令奎, 黄议乐, 杨印庆, 陈姝敏, 张亢, 李良俊, 程锋. 7种茄科植物染色体的演化关系研究[J]. 园艺学报, 2023, 50(5): 1009-1024.

FU Yu, ZHANG Lingkui, HUANG Yile, YANG Yinqing, CHEN Shumin, ZHANG Kang, LI Liangjun, CHENG Feng. The Evolutionary Relationship of Chromosomes in Seven Solanaceae Species[J]. Acta Horticulturae Sinica, 2023, 50(5): 1009-1024.

图/表 7

表1 基因组信息

Table 1 Information of genomes

物种 Species	染色体数 Chromosome number	品种名/版本 Cultivar name/Version	染色体上基因数 Gene number
番茄 Solanum lycopersicum	12	SL4.0	33 562
马铃薯 Solanum tuberosum	12	DM v6.1	32 819
茄子 Solanum melongena	12	V4.1	33 644
辣椒 Capsicum annuum	12	CM334	31 600
菇娘果 Physalis floridana	12	V1	31 878
枸杞 Lycium barbarum	12	V1	33 431
烟草 Nicotiana tabacum	24	NIATTr2	35 519
葡萄 Vitis vinifera	19	12X	26 588
咖啡 Coffea canephora	11	V1	25 574

图1 茄科物种基因组进化特征以及比较基因组分析 A：茄科植物与参照物种的系统发育树及基因家族扩张与收缩情况（红色星表示WGT-γ事件，绿色星表示WGT-T事件）及已测序的7个茄科植物基因组之间的共线性片段关系。B：茄科物种同源基因的Ks分布图。C：茄科基因之间共线性基因对统计信息（红色字表示共线性基因占红色框中基因组的比例，绿色字表示共线性基因占绿色框中基因组的比例）。

Fig. 1 Genome evolution characteristics and comparative genomic analysis of Solanaceae A：Phylogenetic tree and gene family expansion and contraction of Solanaceae and reference species（red star represents WGT-γ event，green star represents WGT-T event）and collinear fragment relationships among sequenced genomes of seven Solanaceae species. B：The Ks distributions of homologous gene of Solanaceae species. C：Statistical information on intragroup collinear gene pairs among Solanaceae genomes（red fonts represent the proportion of collinear genes in the genome of the red box，and green fonts represent the proportion of collinear genes in the genome of the green box）.

图2 番茄基因组片段（GB）划分规则及分布 A：番茄与其他茄科植物的共线性基因点阵图。B：番茄基因组中27个GB（S1 ~ S27）的分布及着丝粒大体位置（每个GB的颜色由祖先基因组AN5的染色体决定，黑色圆圈表示着丝粒大致位置）。

Fig. 2 Genomic block division rules and distribution of tomato A：Collinear gene dot plot of tomato and other Solanaceae species. B：Distribution of 27 GBs（S1-S27）in tomato genome and general location of centromere（The color of each GB is determined by the chromosomes of the ancestral genome AN5. Black ellipse indicates the approximate location of the centromeres）.

图4 茄科祖先染色体推断过程（A）和茄科祖先染色体在现代染色体的重排轨迹（B）

Fig. 4 The inference process of Solanaceae ancestral chromosomes（A）and the rearrangement track of Solanaceae ancestral chromosomes in modern chromosomes（B）

图3 祖先染色体连接关系的推断规则示例

Fig. 3 Examples of inference rules for ancestral chromosome connectivity relationship

图5 茄科基因组中重组染色体的区域特征（A）和保守染色体的区域特征（B）图中染色体第3行为马铃薯着丝粒序列在茄科物种中最佳匹配序列密度图，黑色圆圈表示着丝粒候选位置。GD：基因密度；BM：最佳匹配度；RD：重复序列密度。

Fig. 5 Regional characteristics of chromosomal rearrangement in Solanaceae（A）and reginal characteristics of recombinant chromosomes in Solanaceae genome（B） The third row of chromosomes in the figure shows the density of the best matching sequence of potato centromere sequences in Solanaceae species. Black ellipse indicates approximate centromere location. GD：Gene density；BM：Best match；RD：Repeat density.

图 6 SlMBP3在茄科各物种的分布

Fig. 6 Distribution of SlMBP3 in various species of Solanaceae

参考文献 67

[1]	Altschul S F, Gish W, Miller W, Myers E W, Lipman D J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215 (3):403-410. doi: 10.1016/S0022-2836(05)80360-2 pmid: 2231712
[2]	Armengol L, Marquès-Bonet T, Cheung J, Khaja R, González J R, Scherer S W, Navarro A, Estivill X. 2005. Murine segmental duplications are hot spots for chromosome and gene evolution. Genomics, 86 (6):692-700. pmid: 16256303
[3]	Bailey J A, Baertsch R, Kent W J, Haussler D, Eichler E E. 2004. Hotspots of mammalian chromosomal evolution. Genome Biology, 5 (4):R23. doi: 10.1186/gb-2004-5-4-r23 pmid: 15059256
[4]	Barchi L, Rabanus - Wallace M T, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino G L, Stein N, Lanteri S, Giuliano G. 2021. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. The Plant Journal, 107 (2):579-596. doi: 10.1111/tpj.15313 pmid: 33964091
[5]	Bell C D, Soltis D E, Soltis P S. 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, 97 (8):1296-1303. doi: 10.3732/ajb.0900346 pmid: 21616882
[6]	Bulazel K V, Ferreri G C, Eldridge M D, O'Neill R J. 2007. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biology, 8 (8):R170. doi: 10.1186/gb-2007-8-8-r170 pmid: 17708770
[7]	Byrne K P, Wolfe K H. 2005. The yeast gene order browser:combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research, 15 (10):1456-1461. doi: 10.1101/gr.3672305 URL
[8]	Cao Y L, Li Y L, Fan Y F, Li Z, Yoshida K, Wang J Y, Ma X K, Wang N, Mitsuda N, Kotake T, Ishimizu T, Tsai K C, Niu S C, Zhang D, Sun W H, Luo Q, Zhao J H, Yin Y, Zhang B, Wang J Y, Qin K, An W, He J, Dai G L, Wang Y J, Shi Z G, Jiao E N, Wu P J, Liu X, Liu B, Liao X Y, Jiang Y T, Yu X, Hao Y, Xu X Y, Zou S Q, Li M H, Hsiao Y Y, Lin Y F, Liang C K, Chen Y Y, Wu W L, Lu H C, Lan S R, Wang Z W, Zhao X, Zhong W Y, Yeh C M, Tsai W C, van de Peer Y, Liu Z J. 2021. Wolfberry genomes and the evolution of Lycium(Solanaceae). Communications Biology, 4 (1):671. doi: 10.1038/s42003-021-02152-8
[9]	Cheng F, Wu J, Fang L, Wang X. 2012. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Frontiers in Plant Science, 3:198. doi: 10.3389/fpls.2012.00198 pmid: 22969786
[10]	Coghlan A, Eichler E E, Oliver S G, Paterson A H, Stein L. 2005. Chromosome evolution in eukaryotes:a multi-kingdom perspective. Trends in Genetics, 21 (12):673-682. doi: 10.1016/j.tig.2005.09.009 pmid: 16242204
[11]	Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury J M, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes M C, Crouzillat D, da Silva C, Daddiego L, de Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joet T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li L T, Librado P, Lopez L, Munoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant - Dubreuil C, van Buren R, Zhang Q, Andrade A C, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry R J, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert V A, Wincker P, Lashermes P. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345 (6201):1181-1184. doi: 10.1126/science.1255274 pmid: 25190796
[12]	Edgar R. 2021. MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping. BioRxiv,449169.
[13]	Edwards K D, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans A D, Bombarely A, Allen F, Hurst R, White B, Kernodle S P, Bromley J R, Sanchez-Tamburrino J P, Lewis R S, Mueller L A. 2017. A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics, 18 (1):448. doi: 10.1186/s12864-017-3791-6 pmid: 28625162
[14]	Emms D M, Kelly S. 2019. OrthoFinder:phylogenetic orthology inference for comparative genomics. Genome Biology, 20 (1):238. doi: 10.1186/s13059-019-1832-y
[15]	Flynn J M, Hubley R, Goubert C, Rosen J, Clark A G, Feschotte C, Smit A F. 2020. RepeatModeler 2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences, 117 (17):9451-9457.
[16]	Freeling M, Scanlon M J, Fowler J E. 2015. Fractionation and subfunctionalization following genome duplications:mechanisms that drive gene content and their consequences. Current Opinion in Genetics & Development, 35:110-118.
[17]	Hampson S E, Gaut B S, Baldi P. 2005. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics, 21 (8):1339-1348. pmid: 15585535
[18]	Han M V, Thomas G W, Lugo-Martinez J, Hahn M W. 2013. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution, 30 (8):1987-1997. doi: 10.1093/molbev/mst100 pmid: 23709260
[19]	Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H. 2014. Draft genome sequence of eggplant(Solanum melongena L.) the representative solanum species indigenous to the old world. DNA Research, 21 (6):649-660. doi: 10.1093/dnares/dsu027 pmid: 25233906
[20]	Hosmani P S, Flores-Gonzalez M, Geest H V D, Maumus F, Saha S. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing,Hi-C proximity ligation and optical maps. BioRxiv,767764.
[21]	Huang B, Hu G, Wang K, Frasse P, Maza E, Djari A, Deng W, Pirrello J, Burlat V, Pons C, Granell A, Li Z, van der Rest B, Bouzayen M. 2021. Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes. Nature Communication, 12 (1):6892. doi: 10.1038/s41467-021-27117-7
[22]	Huang G, Zhu Y X. 2019. Plant polyploidy and evolution. Journal of Integrative Plant Biology, 61 (1):4-6. doi: 10.1111/jipb.12758
[23]	Jagannathan M, Cummings R, Yamashita Y M. 2018. A conserved function for pericentromeric satellite DNA. eLife, 7:e34122. doi: 10.7554/eLife.34122 URL
[24]	Jiao Y, Wickett N J, Ayyampalayam S, Chanderbali A S, Landherr L, Ralph P E, Tomsho L P, Hu Y, Liang H, Soltis P S, Soltis D E, Clifton S W, Schlarbaum S E, Schuster S C, Ma H, Leebens-Mack J, dePamphilis C W. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature, 473 (7345):97-100. doi: 10.1038/nature09916
[25]	Kapun M, Flatt T. 2019. The adaptive significance of chromosomal inversion polymorphisms in Drosophila melanogaster. Molecular Ecology Resources, 28 (6):1263-1282.
[26]	Kehrer-Sawatzki H, Sandig C A, Goidts V, Hameister H. 2005. Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans. Cytogenetic and Genome Research, 108 (1-3):91-97. pmid: 15545720
[27]	Kim S, Park J, Yeom S I, Kim Y M, Seo E, Kim K T, Kim M S, Lee J M, Cheong K, Shin H S, Kim S B, Han K, Lee J, Park M, Lee H A, Lee H Y, Lee Y, Oh S, Lee J H, Choi E, Choi E, Lee S E, Jeon J, Kim H, Choi G, Song H, Lee J, Lee S C, Kwon J K, Lee H Y, Koo N, Hong Y, Kim R W, Kang W H, Huh J H, Kang B C, Yang T J, Lee Y H, Bennetzen J L, Choi D. 2017. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biology, 18 (1):210. doi: 10.1186/s13059-017-1341-9 pmid: 29089032
[28]	Kumar S, Stecher G, Suleski M, Hedges S B. 2017. Timetree:a resource for timelines,timetrees,and divergence times. Molecular Ecology Resources, 34 (7):1812-1819.
[29]	Larkin D M, Pape G, Donthu R, Auvil L, Welge M, Lewin H A. 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Research, 19 (5):770-777. doi: 10.1101/gr.086546.108 pmid: 19342477
[30]	Liu L, Zhang K, Bai J, Jinrui B, Lu J H, Lu X X, Hu J L, Pan C Y, He S M, Yuan J L, Zhang Y Y, Zhang M, Guo Y M, Wang X X, Huang Z J, Du Y C, Cheng F, Li J M. 2022. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany, 73:123-138. doi: 10.1093/jxb/erab401 URL
[31]	Luo M C, Deal K R, Akhunov E D, Akhunova A R, Anderson O D, Anderson J A, Blake N, Clegg M T, Coleman-Derr D, Conley E J, Crossman C C, Dubcovsky J, Gill B S, Gu Y Q, Hadam J, Heo H Y, Huo N, Lazo G, Ma Y, Matthews D E, McGuire P E, Morrell P L, Qualset C O, Renfro J, Tabanao D, Talbert L E, Tian C, Toleno D M, Warburton M L, You F M, Zhang W, Dvorak J. 2009. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proceedings of the National Academy of Sciences, 106 (37):15780-15785.
[32]	Martin G B, Brommonschenkel S H, Chunwongse J, Frary A, Tanksley S D. 1993. Map - based cloning of a protein kinase gene conferring disease resistance in tomato. Science, 262 (5138):1432-1436. doi: 10.1126/science.7902614 pmid: 7902614
[33]	Masterson J. 1994. Stomatal size in fossil plants:evidence for polyploidy in majority of angiosperms. Science, 264 (5157):421-424. doi: 10.1126/science.264.5157.421 pmid: 17836906
[34]	Melters D P, Bradnam K R, Young H A, Telis N, May M R, Ruby J G, Sebra R, Peluso P, Eid J, Rank D, Garcia J F, DeRisi J L, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan S W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology, 14 (1):R10. doi: 10.1186/gb-2013-14-1-r10 URL
[35]	Murat F, Xu J H, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J. 2010. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research, 20 (11):1545-1557. doi: 10.1101/gr.109744.110 pmid: 20876790
[36]	Olmstead R G, Bohs L. 2007. A summary of molecular systematic research in Solanaceae:1982-2006. Acta Horticulturae, 745:255-268.
[37]	Ou S, Jiang N. 2018. LTR_retriever:a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology, 176 (2):1410-1422. doi: 10.1104/pp.17.01310 URL
[38]	Padmanabhan S, Thakur J, Siddharthan R, Sanyal K. 2008. Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts,Candida albicans and Candida dubliniensis. Proceedings of the National Academy of Sciences, 105 (50):19797-19802.
[39]	Pham G M, Hamilton J P, Wood J C, Burke J T, Zhao H, Vaillancourt B, Ou S, Jiang J, Buell C R. 2020. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience, 9 (9):giaa100. doi: 10.1093/gigascience/giaa100 URL
[40]	Qian Ming. 1983. A brief introduction to plant of Solanaceae. Biology teaching. Shanghai: East China Normal University. (in Chinese)
	钱明. 1983. 茄科植物简介. 生物学教学. 上海: 华东师范大学.
[41]	Ramos M J N, Coito J L, Faisca-Silva D, Cunha J, Costa M M R, Amancio S, Rocheta M. 2020. Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris). Scientific Reports, 10 (1):18993. doi: 10.1038/s41598-020-76012-6 pmid: 33149248
[42]	Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, van de Peer Y, Persson S. 2017. Revisiting ancestral polyploidy in plants. Science Advances, 3 (7):e1603195. doi: 10.1126/sciadv.1603195 URL
[43]	Salse J. 2016. Ancestors of modern plant crops. Current Opinion in Plant Biology, 30:134-142. doi: 10.1016/j.pbi.2016.02.005 pmid: 26985732
[44]	Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close Timothy J, Messing J, Feuillet C. 2009a. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proceedings of the National Academy of Sciences, 106 (35):14908-14913.
[45]	Salse J, Abrouk M, Murat F, Quraishi U M, Feuillet C. 2009b. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Briefings In Bioinformatics, 10 (6):619-630. doi: 10.1093/bib/bbp037 URL
[46]	Sanderson M J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19 (2):301-302. doi: 10.1093/bioinformatics/19.2.301 pmid: 12538260
[47]	Sankoff D, Goldstein M. 1989. Probabilistic models of genome shuffling. Bulletin of Mathematical Biology, 51 (1):117-124. pmid: 2706396
[48]	Schnable J C, Freeling M, Lyons E. 2012. Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution, 4 (3):265-277. doi: 10.1093/gbe/evs009 pmid: 22275519
[49]	Schubert I, Lysak M A. 2011. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends In Genetics, 27 (6):207-216. doi: 10.1016/j.tig.2011.03.004 pmid: 21592609
[50]	Schwartz M, Zlotorynski E, Kerem B. 2006. The molecular basis of common and rare fragile sites. Cancer Letters, 232 (1):13-26. pmid: 16236432
[51]	Shimizu-Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu K K. 2017. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Molecular Ecology, 26 (1):193-207. doi: 10.1111/mec.13738 pmid: 27352992
[52]	Soltis P S, Marchant D B, van de peer Y, Soltis D E. 2015. Polyploidy and genome evolution in plants. Current Opinion in Genetics & Development, 35:119-125.
[53]	Soltis P S, Soltis D E. 2016. Ancient WGD events as drivers of key innovations in angiosperms. Current Opinion in Plant Biology, 30:159-165. doi: 10.1016/j.pbi.2016.03.015 pmid: 27064530
[54]	Stamatakis A. 2014. RAxML version 8:a tool for phylogenetic analysis and post - analysis of large phylogenies. Bioinformatics, 30 (9):1312-1313. doi: 10.1093/bioinformatics/btu033 URL
[55]	Su H, Liu Y, Liu C, Shi Q, Huang Y, Han F. 2019. Centromere satellite repeats have undergone rapid changes in polyploid wheat subgenomes. Plant Cell, 31 (9):2035-2051. doi: 10.1105/tpc.19.00133 URL
[56]	Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics, 4:10.
[57]	The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400):635-641. doi: 10.1038/nature11119
[58]	van de Peer Y, Mizrachi E, Marchal K. 2017. The evolutionary significance of polyploidy. Nature Reviews Genetics, 18 (7):411-424. doi: 10.1038/nrg.2017.26 pmid: 28502977
[59]	Vollger M R, Guitart X, Dishuck P C, Mercuri L, Harvey W T, Gershman A, Diekhans M, Sulovari A, Munson K M, Lewis A P, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga K H, Phillippy A M, Timp W, Ventura M, Eichler E E. 2022. Segmental duplications and their variation in a complete human genome. Science, 376:6588.
[60]	Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley S D. 2008. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180 (1):391-408. doi: 10.1534/genetics.108.087981 pmid: 18723883
[61]	Wikstrom N, Savolainen V, Chase M W. 2001. Evolution of the angiosperms:calibrating the family tree. Proceedings of the Royal Society B:Biological Sciences, 268 (1482):2211-2220.
[62]	Wu F, Mueller L A, Crouzillat D, Pétiard V, Tanksley S D. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes(COSII)for comparative,evolutionary and systematic studies:a test case in the euasterid plant clade. Genetics, 174 (3):1407-1420. doi: 10.1534/genetics.106.062455 URL
[63]	Wu F, Tanksley S D. 2010. Chromosomal evolution in the plant family Solanaceae. BMC Genomics, 11:182. doi: 10.1186/1471-2164-11-182 pmid: 20236516
[64]	Yadav V, Sun S, Billmyre R B, Thimmappa B C, Shea T, Lintner R, Bakkeren G, Cuomo C A, Heitman J, Sanyal K. 2018. RNAi is a critical determinant of centromere evolution in closely related fungi. Proceedings of the National Academy of Sciences, 115 (12):3108-3113.
[65]	Zhang K, Wang X W, Cheng F. 2019. Plant polyploidy:origin,evolution,and its influence on crop domestication. Horticultural Plant Journal, 5 (6):231-239. doi: 10.1016/j.hpj.2019.11.003
[66]	Zhang Z. 2022. KaKs_calculator 3.0:Calculating selective pressure on coding and non-coding sequences. Genomics Proteomics & Bioinformatics, 20 (3):536-540.
[67]	Zheng C, Zhu Q, Sankoff D. 2007. Genome halving with an outgroup. Evolutionary Bioinformatics, 2:295-302.