Origin and Evolution of Diploid and Allopolyploid Camelina Genomes Were Accompanied by Chromosome Shattering

. 2019 Nov ; 31 (11) : 2596-2612. [epub] 20190826

Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid31451448

Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (Camelina sativa), an important hexaploid oilseed crop closely related to Arabidopsis (Arabidopsis thaliana), the putative parental species as well as the origin of other Camelina species remained unknown. By using bacterial artificial chromosome-based chromosome painting, genomic in situ hybridization, and multi-gene phylogenetics, we aimed to elucidate the origin and evolution of the polyploid complex. Genomes of diploid camelinas (Camelina hispida, n = 7; Camelina laxa, n = 6; and Camelina neglecta, n = 6) originated from an ancestral n = 7 genome. The allotetraploid genome of Camelina rumelica (n = 13, N6H) arose from hybridization between diploids related to C. neglecta (n = 6, N6) and C. hispida (n = 7, H), and the N subgenome has undergone a substantial post-polyploid fractionation. The allohexaploid genomes of C. sativa and Camelina microcarpa (n = 20, N6N7H) originated through hybridization between an auto-allotetraploid C. neglecta-like genome (n = 13, N6N7) and C. hispida (n = 7, H), and the three subgenomes have remained stable overall since the genome merger. Remarkably, the ancestral and diploid Camelina genomes were shaped by complex chromosomal rearrangements, resembling those associated with human disorders and resulting in the origin of genome-specific shattered chromosomes.plantcell;31/11/2596/FX1F1fx1.

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Augustin J.M., Higashi Y., Feng X., Kutchan T.M. (2015). Production of mono- and sesquiterpenes in PubMed

Augustin M.M., Shukla A.K., Starks C.M., O’Neil-Johnson M., Han L., Holland C.K., Kutchan T.M. (2017). Biosynthesis of

Beilstein M.A., Al-Shehbaz I.A., Kellogg E.A. (2006). Brassicaceae phylogeny and trichome evolution. Am. J. Bot. 93: 607–619. PubMed

Beilstein M.A., Al-Shehbaz I.A., Mathews S., Kellogg E.A. (2008). Brassicaceae phylogeny inferred from phytochrome A and PubMed

Bird K.A., VanBuren R., Puzey J.R., Edger P.P. (2018). The causes and consequences of subgenome dominance in hybrids and recent polyploids. New Phytol. 220: 87–93. PubMed

Bolger A.M., Lohse M., Usadel B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. PubMed PMC

Brock J.R., Dönmez A.A., Beilstein M.A., Olsen K.M. (2018). Phylogenetics of PubMed

Brock J.R., Mandáková T., Lysak M.A., Al-Shehbaz I.A. (2019). PubMed PMC

Clark J.W., Donoghue P.C.J. (2017). Constraining the timing of whole genome duplication in plant evolutionary history. Proc. Biol. Sci. 284: 20170912. PubMed PMC

Douglas G.M., et al. (2015). Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid PubMed PMC

Edger P.P., et al. (2019). Origin and evolution of the octoploid strawberry genome. Nat. Genet. 51: 541–547. PubMed PMC

El Baidouri M., Murat F., Veyssiere M., Molinier M., Flores R., Burlot L., Alaux M., Quesneville H., Pont C., Salse J. (2017). Reconciling the evolutionary origin of bread wheat ( PubMed

Endo T.R. (1990). Gametocidal chromosomes and their induction of chromosome mutations in wheat. Jpn. J. Genet. 65: 135–152.

Forment J.V., Kaidi A., Jackson S.P. (2012). Chromothripsis and cancer: Causes and consequences of chromosome shattering. Nat. Rev. Cancer 12: 663–670. PubMed

Franzke A., Lysak M.A., Al-Shehbaz I.A., Koch M.A., Mummenhoff K. (2011). Cabbage family affairs: The evolutionary history of Brassicaceae. Trends Plant Sci. 16: 108–116. PubMed

Freeling M., Woodhouse M.R., Subramaniam S., Turco G., Lisch D., Schnable J.C. (2012). Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15: 131–139. PubMed

Fukami M., Shima H., Suzuki E., Ogata T., Matsubara K., Kamimaki T. (2017). Catastrophic cellular events leading to complex chromosomal rearrangements in the germline. Clin. Genet. 91: 653–660. PubMed

Gaebelein R., Mason A.S. (2018). Allohexaploids in the genus

Gaeta R.T., Chris Pires J. (2010). Homoeologous recombination in allopolyploids: The polyploid ratchet. New Phytol. 186: 18–28. PubMed

Garsmeur O., Schnable J.C., Almeida A., Jourda C., D’Hont A., Freeling M. (2014). Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol. 31: 448–454. PubMed

Gehringer A., Friedt W., Lühs W., Snowdon R.J. (2006). Genetic mapping of agronomic traits in false flax ( PubMed

Hu Y., et al. (2019). PubMed

Huson D.H., Scornavacca C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61: 1061–1067. PubMed

Hutcheon C., Ditt R.F., Beilstein M., Comai L., Schroeder J., Goldstein E., Shewmaker C.K., Nguyen T., De Rocher J., Kiser J. (2010). Polyploid genome of PubMed PMC

Iskandarov U., Kim H.J., Cahoon E.B. (2014).

Iven T., Hornung E., Heilmann M., Feussner I. (2016). Synthesis of oleyl oleate wax esters in PubMed PMC

Ivkov R., Bunz F. (2015). Pathways to chromothripsis. Cell Cycle 14: 2886–2890. PubMed PMC

Jiang W.Z., Henry I.M., Lynagh P.G., Comai L., Cahoon E.B., Weeks D.P. (2017). Significant enhancement of fatty acid composition in seeds of the allohexaploid, PubMed PMC

Jiao Y., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97–100. PubMed

Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJC, Wickett NJ. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant. Sci. 4: apps.1600016. PubMed PMC

Junier T., Zdobnov E.M. (2010). The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26: 1669–1670. PubMed PMC

Kagale S., et al. (2014). The emerging biofuel crop PubMed PMC

Katoh K., Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772–780. PubMed PMC

Kocsis E., Trus B.L., Steer C.J., Bisher M.E., Steven A.C. (1991). Image averaging of flexible fibrous macromolecules: The clathrin triskelion has an elastic proximal segment. J. Struct. Biol. 107: 6–14. PubMed

Korbel J.O., Campbell P.J. (2013). Criteria for inference of chromothripsis in cancer genomes. Cell 152: 1226–1236. PubMed

Krzywinski M., Schein J., Birol I., Connors J., Gascoyne R., Horsman D., Jones S.J., Marra M.A. (2009). Circos: An information aesthetic for comparative genomics. Genome Res. 19: 1639–1645. PubMed PMC

Kyriakidou M., Tai H.H., Anglin N.L., Ellis D., Strömvik M.V. (2018). Current strategies of polyploid plant genome sequence assembly. Front. Plant Sci. 9: 1660. PubMed PMC

Landis J.B., Soltis D.E., Li Z., Marx H.E., Barker M.S., Tank D.C., Soltis P.S. (2018). Impact of whole-genome duplication events on diversification rates in angiosperms. Am. J. Bot. 105: 348–363. PubMed

Lu C., Kang J. (2008). Generation of transgenic plants of a potential oilseed crop PubMed

Luo Z., Brock J., Dyer J.M., Kutchan T., Schachtman D., Augustin M., Ge Y., Fahlgren N., Abdel-Haleem H. (2019). Genetic diversity and population structure of PubMed PMC

Lysak M.A., Berr A., Pecinka A., Schmidt R., McBreen K., Schubert I. (2006). Mechanisms of chromosome number reduction in PubMed PMC

Lysak M.A., Mandáková T., Schranz M.E. (2016). Comparative paleogenomics of crucifers: Ancestral genomic blocks revisited. Curr. Opin. Plant Biol. 30: 108–115. PubMed

Maher C.A., Wilson R.K. (2012). Chromothripsis and human disease: Piecing together the shattering process. Cell 148: 29–32. PubMed PMC

Mandáková T., Kovarík A., Zozomová-Lihová J., Shimizu-Inatsugi R., Shimizu K.K., Mummenhoff K., Marhold K., Lysak M.A. (2013). The more the merrier: Recent hybridization and polyploidy in PubMed PMC

Mandáková T., Lysak M.A. (2016a). Chromosome preparation for cytogenetic analyses in Arabidopsis. Curr. Protoc. Plant Biol. 1: 43–51. PubMed

Mandáková T., Lysak M.A. (2016b). Painting of PubMed

Mandáková T., Marhold K., Lysak M.A. (2014). The widespread crucifer species PubMed

Mandáková T., Pouch M., Harmanová K., Zhan S.H., Mayrose I., Lysak M.A. (2017). Multispeed genome diploidization and diversification after an ancient allopolyploidization. Mol. Ecol. 26: 6445–6462. PubMed

Mandáková T., Schranz M.E., Sharbel T.F., de Jong H., Lysak M.A. (2015). Karyotype evolution in apomictic PubMed

Mandáková T., Zozomová-Lihová J., Kudoh H., Zhao Y., Lysak M.A., Marhold K. (2019). The story of promiscuous crucifers: Origin and genome evolution of an invasive species, PubMed PMC

Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B., Steuernagel B., Mayer K.F., Olsen O.A.; International Wheat Genome Sequencing Consortium (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science 345: 1250092. PubMed

Mason A.S., Snowdon R.J. (2016). Oilseed rape: Learning about ancient and recent polyploid evolution from a recent crop species. Plant Biol (Stuttg) 18: 883–892. PubMed

Morineau C., Bellec Y., Tellier F., Gissot L., Kelemen Z., Nogué F., Faure J.D. (2017). Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid PubMed PMC

Martin S.L., Lujan-Toro B.E., Sauder C.A., James T., Ohadi S., Hall L.M. (2018). Hybridization rate and hybrid fitness for PubMed PMC

Moser B.R. (2012). Biodiesel from alternative oilseed feedstocks:

Nagaharu U., Nagaharu N. (1935). Genome analysis in

Nasuda S., Friebe B., Gill B.S. (1998). Gametocidal genes induce chromosome breakage in the interphase prior to the first mitotic cell division of the male gametophyte in wheat. Genetics 149: 1115–1124. PubMed PMC

Nikolov L.A., Shushkov P., Nevado B., Gan X., Al-Shehbaz I.A., Filatov D., Bailey C.D., Tsiantis M. (2019). Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytol. 222: 1638–1651. PubMed

Novikova P.Y., et al. (2017). Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol. Biol. Evol. 34: 957–968. PubMed PMC

Ozseyhan M.E., Kang J., Mu X., Lu C. (2018). Mutagenesis of the FAE1 genes significantly changes fatty acid composition in seeds of PubMed

Parisod C., Holderegger R., Brochmann C. (2010). Evolutionary consequences of autopolyploidy. New Phytol. 186: 5–17. PubMed

Paterson A.H., et al. (2012). Repeated polyploidization of PubMed

Pellestor F., Gatinois V. (2019). Chromothripsis, a credible chromosomal mechanism in evolutionary process. Chromosoma 128: 1–6. PubMed

Rabiee M., Sayyari E., Mirarab S. (2019). Multi-allele species reconstruction using ASTRAL. Mol. Phylogenet. Evol. 130: 286–296. PubMed

Renny-Byfield S., Kovarik A., Kelly L.J., Macas J., Novak P., Chase M.W., Nichols R.A., Pancholi M.R., Grandbastien M.A., Leitch A.R. (2013). Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. Plant J. 74: 829–839. PubMed

Ruiz-Lopez N., Haslam R.P., Napier J.A., Sayanova O. (2014). Successful high-level accumulation of fish oil omega-3 long-chain polyunsaturated fatty acids in a transgenic oilseed crop. Plant J. 77: 198–208. PubMed PMC

Salmon A., Ainouche M.L., Wendel J.F. (2005). Genetic and epigenetic consequences of recent hybridization and polyploidy in PubMed

Séguin‐Swartz G., Nettleton J.A., Sauder C., Warwick S.I., Gugel R.K. (2013). Hybridization between

Shaw T.I., Ruan Z., Glenn T.C., Liu L. (2013). STRAW: Species TRee Analysis Web server. Nucleic Acids Res. 41: W238-41. PubMed PMC

Shonnard D.R., Williams L., Kalnes T.M. (2010).

Sierro N., Battey J.N., Ouadi S., Bakaher N., Bovet L., Willig A., Goepfert S., Peitsch M.C., Ivanov N.V. (2014). The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 5: 3833. PubMed PMC

Smith S.A., Dunn C.W. (2008). Phyutility: A phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715–716. PubMed

Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313. PubMed PMC

Stebbins G.L. (1971). Chromosomal Evolution in Higher Plants.. (London: Edward Arnold; ).

Stephens P.J., et al. (2011). Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144: 27–40. PubMed PMC

Stockenhuber R., Zoller S., Shimizu-Inatsugi R., Gugerli F., Shimizu K.K., Widmer A., Fischer M.C. (2015). Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing. PLoS One 10: e0128181. PubMed PMC

Sun H., et al. (2017). Karyotype stability and unbiased fractionation in the paleo-allotetraploid PubMed

Symonds V.V., Soltis P.S., Soltis D.E. (2010). Dynamics of polyploid formation in PubMed

Tan E.H., Henry I.M., Ravi M., Bradnam K.R., Mandakova T., Marimuthu M.P., Korf I., Lysak M.A., Comai L., Chan S.W. (2015). Catastrophic chromosomal restructuring during genome elimination in plants. eLife 4: e06516. PubMed PMC

VanBuren R., Wai C.M., Pardo J., Yocca A.E., Wang X., Wang H., Chaluvadi S.R., Bryant D., Edger P.E., Bennetzen J.L., Mockler T.C., Michael T.P. (2019). Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. bioRxiv (preprint) 10.1101/580720. PubMed PMC

Vollmann J., Grausgruber H., Stift G., Dryzhyruk C., Lelley T. (2005). Genetic diversity in

Waltz E. (2018). With a free pass, CRISPR-edited plants reach market in record time. Nat. Biotechnol. 36: 6–7. PubMed

Wang X., et al. ; Brassica rapa Genome Sequencing Project Consortium (2011). The genome of the mesopolyploid crop species PubMed

Wen D., Yu Y., Zhu J., Nakhleh L. (2018). Inferring phylogenetic networks using PhyloNet. Syst. Biol. 67: 735–740. PubMed PMC

Yang J., et al. (2016). The genome sequence of allopolyploid PubMed

Zhang P., Li W., Friebe B., Gill B.S. (2008). The origin of a “zebra” chromosome in wheat suggests nonhomologous recombination as a novel mechanism for new chromosome evolution and step changes in chromosome number. Genetics 179: 1169–1177. PubMed PMC

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