植物古基因组学研究进展

doi:10.16288/j.yczz.17-191

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Hereditas(Beijing) ›› 2018, Vol. 40 ›› Issue (1): 44-56.doi: 10.16288/j.yczz.17-191

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Progress in plant paleogenomics

Taikui Zhang^1,²(),Zhaohe Yuan^1,²

1. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2. College of Forestry, Nanjing Forestry University, Nanjing 210037, China

Received:2017-05-25 Revised:2017-09-04 Online:2018-01-20 Published:2017-12-22
Supported by:
the Initiative Project for Talents of Nanjing Forestry University(GXL2014070);the Doctorate Fellowship Foundation of Nanjing Forestry University;the Research Fund for Postgraduate Innovation Project of Jiangsu Province(KYLX16_0857);the Priority Academic Program Development of Jiangsu High Education Institutions (PAPD)

Abstract

Abstract:

As a new branch of genomics, plant paleogenomics reconstructs ancestral genomes from actual modern species and infers palaeohistory, evolutionary and/or speciation events that have shaped the modern species. Advances in high-throughput sequencing technologies yield accurate long reads, promote the progress of plant genome sequence assembly, and thereby offer paleogenomics a large collection of valuable reference genomes from modern species. Whole-genome duplication (WGD) and polyploidization cause rapid genomic reorganization, massive gene losses and structural variations. WGD events are therefore central to plant evolution. In this review, we summarize recent progress in sequencing and assembly of plant genomes, principles of plant paleogenomics, WGD events in plant genomes, and the most likely evolutionary scenario in plants. Furthermore, we highlight some of the challenges as well as future directions.

Key words: plant genome, sequence and assembly, paleogenomics, whole-genome duplication, polyploidization

Taikui Zhang, Zhaohe Yuan. Progress in plant paleogenomics[J]. Hereditas(Beijing), 2018, 40(1): 44-56.

References

[1]	Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J. Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci, 2010, 15(9): 479-487.
[2]	Salse J, Abrouk M, Murat F, Quraishi UM, Feuillet C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform, 2009, 10(6): 619-630.
[3]	Jiao WB, Schneeberger K. The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol, 2017, 36: 64-70.
[4]	Xu Q, Chen LL, Ruan XA, Chen DJ, Zhu AD, Chen CL, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen JJ, Gao S, Xing F, Lan H, Chang JW, Ge XH, Lei Y, Hu Q, Miao Y, Wang L, Xiao SX, Biswas MK, Zeng WF, Guo F, Cao HB, Yang XM, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang ZH, Guo WW, Kuang HH, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan YJ. The draft genome of sweet orange (Citrus sinensis). Nat Genet, 2013, 45: 59-66.
[5]	Huang SW, Li RQ, Zhang ZH, Li L, Gu XF, Fan W, Lucas WJ, Wang XW, Xie BY, Ni PX, Ren YY, Zhu HM, Li J, Lin K, Jin WW, Fei ZJ, Li GC, Staub J, Kilian A, van der Vossen EAG, Wu Y, Guo J, He J, Jia ZQ, Ren Y, Tian G, Lu Y, Ruan J, Qian WB, Wang MW, Huang QF, Li B, Xuan ZL, Cao JJ, Wu ZG, Zhang JB, Cai QL, Bai YQ, Zhao BW, Han YH, Li Y, Li XF, Wang SH, Shi QX, Liu SQ, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng ZC, Zhang SP, Wu J, Yang YH, Kang HX, Li M, Liang HQ, Ren XL, Shi ZB, Wen M, Jian M, Yang HL, Zhang GJ, Yang ZT, Chen R, Liu SF, Li JW, Ma LJ, Liu H, Zhou Y, Zhao J, Fang XD, Li GQ, Fang L, Li YR, Liu DY, Zheng HK, Zhang Y, Qin N, Li Z, Yang GH, Yang S, Bolund L, Kristiansen K Zheng HC, Li SC, Zhang XQ, Yang HM, Wang J, Sun RF, Zhang BX, Jiang SZ, Wang J, Du YC, Li SG. The genome of the cucumber,Cucumis sativus L. Nat Genet, 2009, 41(12): 1275-1281.
[6]	Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan ARK, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Kulheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J. The genome ofEucalyptus grandis. Nature, 2014, 510(7505): 356-362.
[7]	Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, T?pel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Bostr?m C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Sch

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