Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species.
Arachis species
Athila retroelements
Genome differentiation
Genome size variation
Satellite DNA
Journal
Planta
ISSN: 1432-2048
Titre abrégé: Planta
Pays: Germany
ID NLM: 1250576
Informations de publication
Date de publication:
27 Jul 2022
27 Jul 2022
Historique:
received:
21
03
2022
accepted:
12
07
2022
entrez:
27
7
2022
pubmed:
28
7
2022
medline:
30
7
2022
Statut:
epublish
Résumé
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
Identifiants
pubmed: 35895167
doi: 10.1007/s00425-022-03961-9
pii: 10.1007/s00425-022-03961-9
doi:
Substances chimiques
DNA, Satellite
0
Heterochromatin
0
Retroelements
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
50Subventions
Organisme : Fondo para la Investigación Científica y Tecnológica
ID : PICT 2017- 3220
Organisme : Fondo para la Investigación Científica y Tecnológica
ID : PICT 2018-3664
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Alioto T, Alexiou KG, Bardil A et al (2020) Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J 101:455–472
pubmed: 31529539
doi: 10.1111/tpj.14538
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
pubmed: 2231712
doi: 10.1016/S0022-2836(05)80360-2
Ambrožová K, Mandáková T, Bureš P, Neumann P, Leitch IJ, Koblížková A, Macas J, Lysak MA (2011) Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies. Ann Bot 107:255–268
pubmed: 21156758
doi: 10.1093/aob/mcq235
Ammiraju JS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA (2007) Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52:342–351
pubmed: 17764506
doi: 10.1111/j.1365-313X.2007.03242.x
Bechara MD, Moretzsohn MC, Palmieri DA, Monteiro JP, Bacci M, Martins J, Valls JFM, Lopes CR, Gimenes MA (2010) Phylogenetic relationships in genus Arachis based on ITS and 5.8 S rDNA sequences. BMC Plant Biol 10:255
pubmed: 21092103
pmcid: 3095334
doi: 10.1186/1471-2229-10-255
Bennett MD (1987) Variation in genomic form in plants and its ecological implications. New Phytol 106:177–200
doi: 10.1111/j.1469-8137.1987.tb04689.x
Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627
pubmed: 16219458
doi: 10.1016/j.gde.2005.09.010
Bennetzen JL, Kellogg EA (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9:1509–1514
pubmed: 12237393
pmcid: 157029
doi: 10.2307/3870439
Bennetzen JL, Wang H (2014) The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol 65:505–530
pubmed: 24579996
doi: 10.1146/annurev-arplant-050213-035811
Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee TH, Leal-Bertioli SCM, Kim C, Guimarães PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P, Araujo ACG (2013) The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. Ann Bot 112:545–559
pubmed: 23828319
pmcid: 3718217
doi: 10.1093/aob/mct128
Bertioli DJ, Cannon SB, Froenicke L et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 8:438–446
doi: 10.1038/ng.3517
Bertioli DJ, Jenkins J, Clevenger J et al (2019) The genome of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51:877–884
pubmed: 31043755
doi: 10.1038/s41588-019-0405-z
Biémont C, Vieira C (2006) Junk DNA as an evolutionary force. Nature 443:521–524
pubmed: 17024082
doi: 10.1038/443521a
Biscotti MA, Olmo E, Heslop-Harrison JP (2015) Repetitive DNA in eukaryotic genomes. Chromosome Res 23:415–420
pubmed: 26514350
doi: 10.1007/s10577-015-9499-z
Bolsheva NL, Melnikova NV, Kirov IV, Dmitriev AA, Krasnov GS, Amosova AV, Samatadze TE, Yurkevich OY, Zoshchuk SA, Kudryavtseva AV, Muravenko OV (2019) Characterization of repeated DNA sequences in genomes of blue-flowered flax. BMC Evol Biol 19:49
pubmed: 30813893
pmcid: 6391757
doi: 10.1186/s12862-019-1375-6
Chenais B, Caruso A, Hiard S, Casse N (2012) The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509:7–15
pubmed: 22921893
doi: 10.1016/j.gene.2012.07.042
Darzentas N (2010) Circoletto: visualizing sequence similarity with Circos. Bioinformatics 26:2620–2621
pubmed: 20736339
doi: 10.1093/bioinformatics/btq484
Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079
pubmed: 12097344
pmcid: 186626
doi: 10.1101/gr.132102
Dhillon SS, Rake AV, Miksche JP (1980) Reassociation kinetics and cytophotometric characterisation of peanut (Arachis hypogaea L.) DNA. Plant Physiol 65:1121–1127
pubmed: 16661344
pmcid: 440494
doi: 10.1104/pp.65.6.1121
Di Rienzo JA, Casanoves F, Balzarini MG, González L, Tablada M, Robledo CW (2013) InfoStat version 2013. Grupo InfoStat, FCA, Universidad Nacional de Córdoba, Argentina. http://www.infostat.com.ar
Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, Piednoël M, Weiss-Schneeweiss H, Leitch AR (2014) Genomic repeat abundances contain phylogenetic signal. Syst Biol 64:112–126
pubmed: 25261464
pmcid: 4265144
doi: 10.1093/sysbio/syu080
Dodsworth S, Chase MW, Särkinen T, Knapp S, Leitch AR (2016) Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae). Biol J Linn Soc 117:96–105
doi: 10.1111/bij.12612
Dodsworth S, Jang TS, Struebig M, Chase MW, Weiss-Schneeweiss H, Leitch AR (2017) Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae). Plant Syst Evol 303:1013–1020
pubmed: 32009724
doi: 10.1007/s00606-016-1356-9
Dogan M, Pouch M, Mandáková T, Hloušková P, Guo X, Winter P, Chumová Z, Van Niekerk A, Mummenhoff K, Al-Shehbaz IA, Mucina L, Lysak MA (2021) Evolution of tandem repeats is mirroring post-polyploid cladogenesis in Heliophila (Brassicaceae). Front Plant Sci 11:1944
doi: 10.3389/fpls.2020.607893
Doležel J, Bartos J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot 95:99–110
pubmed: 15596459
pmcid: 4246710
doi: 10.1093/aob/mci005
El Baidouri M, Panaud O (2013) Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol Evol 5:954–965
pubmed: 23426643
pmcid: 3673626
doi: 10.1093/gbe/evt025
Emadzade K, Jang TS, Macas J, Kovařík A, Novák P, Parker J, Weiss-Schneeweiss H (2014) Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae). Ann Bot 114:1597–1608
pubmed: 25169019
pmcid: 4273535
doi: 10.1093/aob/mcu178
Ewing AD (2015) Transposable element detection from whole genome sequence data. Mob DNA 6:24
pubmed: 26719777
pmcid: 4696183
doi: 10.1186/s13100-015-0055-3
Fernandez A, Krapovickas A (1994) Cromosomas y evolucion en Arachis (Leguminosae). Bonplandia 8:187–220
doi: 10.30972/bon.81-41499
Ferree PM, Barbash DA (2009) Species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in Drosophila. PLoS Biol 7:e1000234
pubmed: 19859525
pmcid: 2760206
doi: 10.1371/journal.pbio.1000234
Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341
pubmed: 11988759
doi: 10.1038/nrg793
Fransz P, Linc G, Lee CR, Aflitos SA et al (2016) Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J 88:159–178
pubmed: 27436134
pmcid: 5113708
doi: 10.1111/tpj.13262
Friend SA, Quandt D, Tallury SP, Stalker HT, HiluK W (2010) Species, genomes, and section relationships in the genus Arachis (Fabaceae): a molecular phylogeny. Plant Syst Evol 290:185–199
doi: 10.1007/s00606-010-0360-8
Gaiero P, Vaio M, Peters SA, Schranz ME, de Jong H, Speranza PR (2019) Comparative analysis of repetitive sequences among species from the potato and the tomato clades. Ann Bot 123:521–532
pubmed: 30346473
doi: 10.1093/aob/mcy186
Garrido-Ramos MA (2015) Satellite DNA in plants: more than just rubbish. Cytogenet Genome Res 146:153–170
pubmed: 26202574
doi: 10.1159/000437008
Goloboff PA, Farris JS, Nixon K (2008) TNT, a free program for phylogenetic analysis. Cladistics 24:774–786
doi: 10.1111/j.1096-0031.2008.00217.x
Gowda MVC, Bhat RS, Sujay V, Kusuma P, Bhat S, Varshney RK (2011) Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.). Plant Syst Evol 291:153–158
doi: 10.1007/s00606-010-0373-3
Grabiele M, Chalup L, Robledo G, Seijo G (2012) Genetic and geographic origin of domesticated peanut as evidenced by 5S rDNA and chloroplast DNA sequences. Plant Syst Evol 298:1151–1165
doi: 10.1007/s00606-012-0627-3
Gray YH (2000) It takes two transposons to tango. Trends Genet 16:461–468
pubmed: 11050333
doi: 10.1016/S0168-9525(00)02104-1
Gregory MP, Gregory WC (1979) Exotic germoplasm of Arachis L. interspecific hybrids. J Hered 70:185–193
doi: 10.1093/oxfordjournals.jhered.a109231
Greilhuber J, Lysák M, Doležel J, Bennett MD (2005) The origin, evolution and proposed stabilization of the terms ‘genome size’, and ‘C-value’ to describe nuclear DNA contents. Ann Bot 95:255–260
pubmed: 15596473
pmcid: 4246724
doi: 10.1093/aob/mci019
Holland B, Moulton V (2003) Consensus networks: a method for visualising incompatibilities in collections of trees. In: Benson G, Page RDM (eds) International workshop on algorithms in bioinformatics. Springer, Berlin, pp 165–176
doi: 10.1007/978-3-540-39763-2_13
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267
pubmed: 16221896
doi: 10.1093/molbev/msj030
Jurka J, Bao W, Kojima KK (2011) Families of transposable elements, population structure and the origin of species. Biol Direct 6:44
pubmed: 21929767
pmcid: 3183009
doi: 10.1186/1745-6150-6-44
Jurka J, Bao W, Kojima KK, Kohany O, Yurka MG (2012) Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct 7:36
pubmed: 23098210
pmcid: 3500645
doi: 10.1186/1745-6150-7-36
Katoh K, Misasa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 30:3059–3066
pubmed: 12136088
pmcid: 135756
doi: 10.1093/nar/gkf436
Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664
pubmed: 11932250
pmcid: 187518
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
pubmed: 7463489
doi: 10.1007/BF01731581
Krapovickas A, Gregory WC (1994) Taxonomy of the genus Arachis (Leguminosae). Bonplandia 8:1–186
Kreplak J, Madoui MA, Cápal P et al (2019) A reference genome for pea provides insight into legume genome evolution. Nat Genet 51:1411–1422
pubmed: 31477930
doi: 10.1038/s41588-019-0480-1
Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532
pubmed: 10690416
doi: 10.1146/annurev.genet.33.1.479
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
pubmed: 27004904
pmcid: 8210823
doi: 10.1093/molbev/msw054
Lavin M, Schrire BD, Lewis GP, Pennington RT, Delgado-Salinas A, Thulin M, Hughes CE, Beyra-Matos A, Wojciechowski MF (2004) Metacommunity processes rather than continental tectonic history better explain geographically structured phylogenies in legumes. Philos Trans R Soc Lond Biol Sci 359:1509–1522
doi: 10.1098/rstb.2004.1536
Leal-Bertioli SCM, Santos SP, Dantas KM, Inglis PW, Nielen S, Araujo ACG, Silva JP, Cavalcante U, Guimarães PM, Brasileiro ACM, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Moretzsohn MC, Bertioli DJ (2015) Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. Ann Bot 115:237–249
pubmed: 25538110
doi: 10.1093/aob/mcu237
Li W, Zhang P, Fellers JP, Friebe B, Gill BS (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500–511
pubmed: 15500466
doi: 10.1111/j.1365-313X.2004.02228.x
López-Flores I, Garrido-Ramos MA (2012) The repetitive DNA content of eukaryotic genomes. Genome Dyn 7:1–28
pubmed: 22759811
doi: 10.1159/000337118
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410
pubmed: 15240870
pmcid: 515075
doi: 10.1073/pnas.0403715101
Macas J, Novák P, Pellicer J, CíŽková J, KoblíŽková A, Neumann P, Fuková I, Doležel J, Kelly LJ, Leitch IJ (2015) In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe fabeae. PLoS ONE 10:e0143424
pubmed: 26606051
pmcid: 4659654
doi: 10.1371/journal.pone.0143424
Mascagni F, Usai G, Natali L, Cavallini A, Giordani T (2018) A comparison of methods for LTR-retrotransposon insertion time profiling in the Populus trichocarpa genome. Caryologia 71:85–92
doi: 10.1080/00087114.2018.1429749
Mascagni F, Vangelisti A, Giordani T, Cavallini A, Natali L (2020) A computational comparative study of the repetitive DNA in the genus Quercus L. Tree Genet Genomes 16:1–11
doi: 10.1007/s11295-019-1401-2
McCann J, Macas J, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H (2020) Differential genome size and repetitive DNA evolution in diploid species of Melampodium sect. Melampodium (Asteraceae). Front Plant Sci 11:362
pubmed: 32296454
pmcid: 7136903
doi: 10.3389/fpls.2020.00362
Mehrotra S, Goyal V (2014) Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genom Proteom Bioinform 12:164–171
doi: 10.1016/j.gpb.2014.07.003
Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JFM, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11
pmcid: 491793
doi: 10.1186/1471-2229-4-11
Moretzsohn MC, Gouvea EG, Inglis PW, Leal-Bertioli SCM, Valls JFM, Bertioli DJ (2013) A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann Bot 111:113–126
pubmed: 23131301
doi: 10.1093/aob/mcs237
Negm S, Greenberg A, Larracuente AM, Sproul JS (2021) RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles. Mol Ecol Resour 21:969–981
pubmed: 33277787
pmcid: 7954937
doi: 10.1111/1755-0998.13305
Nelson MG, Linheiro RS, Bergman CM (2017) McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data. G3: Genes Genom Genet 7:2763–2778
doi: 10.1534/g3.117.043893
Nielen S, Campos-Fonseca F, Leal-Bertioli SCM, Guimaraes PM, Seijo G, Town C, Arrial R, Bertioli D (2010) FIDEL—a retrovirus-like retrotransposon and its distinct evolutionary histories in the A and B-genome components of cultivated peanut. Chromosome Res 18:227–246
pubmed: 20127167
pmcid: 2844528
doi: 10.1007/s10577-009-9109-z
Nielen S, Vidigal B, Leal-Bertioli SCM, Ratnaparkhe M, Paterson A, Garsmeur O, D’Hont A, Guimaraes P, Bertioli D (2012) Matita, new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A–B genome divergence. Mol Genet Genomics 287:21–38
pubmed: 22120641
doi: 10.1007/s00438-011-0656-6
Noé L, Kucherov G (2005) YASS: enhancing the sensitivity of DNA similarity search. Nucl AcIds Res 33:540–543
doi: 10.1093/nar/gki478
Novák P, Robledillo LA, Koblızková A, Vrbová I, Neumann P, Macas J (2017) TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucl Acids Res 45:e111
pubmed: 28402514
pmcid: 5499541
doi: 10.1093/nar/gkx257
Novák P, Neumann P, Macas J (2020) Global analysis of repetitive DNA from unassembled sequence reads using repeatexplorer2. Nat Protoc 15:3745–3776
pubmed: 33097925
doi: 10.1038/s41596-020-0400-y
Ortiz AM, Robledo G, Seijo G, Valls JFM, Lavia GI (2017) Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section Rhizomatosae and related diploid species (Arachis, Leguminosae). J Plant Res 130:791–807
pubmed: 28536982
doi: 10.1007/s10265-017-0949-x
Paradis E, Schliep K (2018) Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528
doi: 10.1093/bioinformatics/bty633
Patel M, Jung S, Moore K, Powell G, Ainsworth C, Abbott A (2004) High-oleate peanut mutants result from a MITE insertion into the FAD2 gene. Theor Appl Genet 108:1492–1502
pubmed: 14968307
doi: 10.1007/s00122-004-1590-3
Piegu B, Guyot R, Picault N, Roulin A, Sanyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269
pubmed: 16963705
pmcid: 1581435
doi: 10.1101/gr.5290206
Plohl M, Luchetti A, Mestrovic N, Mantovani B (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero) chromatin. Gene 409:72–82
pubmed: 18182173
doi: 10.1016/j.gene.2007.11.013
Plohl M, Meštrović N, Mravinac B (2012) Satellite DNA evolution. Genome Dyn 7:126–152
pubmed: 22759817
doi: 10.1159/000337122
Plohl M, Meštrović N, Mravinac B (2014) Centromere identity from the DNA point of view. Chromosoma 123:313–325
pubmed: 24763964
pmcid: 4107277
doi: 10.1007/s00412-014-0462-0
R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Ren L, Huang W, Cannon EKS, Bertioli DJ, Cannon SB (2018) A mechanism for genome size reduction following genomic rearrangements. Front Genet 9:454–454
pubmed: 30356760
pmcid: 6189423
doi: 10.3389/fgene.2018.00454
Ribeiro T, Vasconcelos E, Dos Santos KGB, Vaio M, Brasileiro-Vidal AC, Pedrosa-Harand A (2020) Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Chromosome Res 28:139–153
pubmed: 31734754
doi: 10.1007/s10577-019-09618-w
Robledillo LA, Koblížkova A, Petr N, Böttinger K, Vrbová I, Neumann P, Schubert I, Macas J (2018) Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing. Sci Rep 8:5838
doi: 10.1038/s41598-018-24196-3
Robledo G, Seijo JG (2008) Characterization of Arachis D genome using physical mapping of heterochromatic regions and rDNA loci by FISH. Genet Mol Biol 31:717–724
doi: 10.1590/S1415-47572008000400019
Robledo G, Seijo G (2010) Species relationships among the wild B genome of Arachis species (section Arachis) based on FISH mapping of rDNA loci and heterochromatin detection: a new proposal for genome arrangement. Theor App Genet 121:1033–1046
doi: 10.1007/s00122-010-1369-7
Robledo G, Lavia GI, Seijo G (2009) Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection. Theor App Genet 118:1295–1307
doi: 10.1007/s00122-009-0981-x
Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A (2021) Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. Planta 253:1–18
doi: 10.1007/s00425-021-03598-0
Samoluk SS, Chalup LMI, Robledo G, Seijo JG (2015a) Genome sizes in diploid and allopolyploid Arachis L. species (section Arachis). Genet Res Crop Evol 62:747–763
doi: 10.1007/s10722-014-0193-3
Samoluk SS, Robledo G, Podio M, Chalup L, Ortiz JPA, Pessino SC, Seijo JG (2015b) First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species. Genetica 143:113–125
pubmed: 25633099
doi: 10.1007/s10709-015-9820-y
Samoluk SS, Robledo G, Bertioli D, Seijo JG (2017) Evolutionary dynamics of an at-rich satellite DNA and its contribution to karyotype differentiation in wild diploid Arachis species. Mol Genet Genomics 292:283–296
pubmed: 27838847
doi: 10.1007/s00438-016-1271-3
Samoluk SS, Chalup LMI, Chavarro C, Robledo G, Bertioli DJ, Jackson SA, Seijo G (2019) Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA. Planta 249:1405–1415
pubmed: 30680457
doi: 10.1007/s00425-019-03096-4
San Miguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot 82:37–44
doi: 10.1006/anbo.1998.0746
Santana SH, Valls JF (2015) Arachis veigae (Fabaceae), the most dispersed wild species of the genus, and yet taxonomically overlooked. Bonplandia 24:139–150
doi: 10.30972/bon.242238
Seijo G, Lavia GI, Fernández A, Krapovickas A, Ducasse D, Moscone EA (2004) Physical mapping of 5S and 18S–25S rRNA genes evidences that Arachis duranensis and A. ipaensis are the wild diploid species involved in the origin of A. hypogaea (Leguminosae). Am J Bot 91:2293–2303
doi: 10.3732/ajb.91.9.1294
Seijo G, Lavia GI, Fernández A, Krapovickas A, Ducasse D, Bertioli DJ, Moscone EA (2007) Genomic relationships between the cultivated peanut (Arachis hypogaea-Leguminosae) and its close relatives revealed by double GISH. Am J Bot 94:1963–1971
pubmed: 21636391
doi: 10.3732/ajb.94.12.1963
Seijo JG, Kovalsky IE, Chalup LMI, Samoluk SS, Fávero A, Robledo G (2018) Karyotype stability and genome specific nucleolar dominance in peanut, its wild 4× ancestor and in a synthetic AABB polyploidy. Crop Sci 58:1671–1683
doi: 10.2135/cropsci2018.02.0088
Seijo GJ, Atahuachi M, Simpson CE, Krapovickas A (2021) Arachis inflata. Bonplandia 30:169–174
doi: 10.30972/bon.3024942
Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12:80
pubmed: 22672714
pmcid: 3404960
doi: 10.1186/1471-2229-12-80
Silva Oliveira MA, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques da Silva SS, Oliveira RS, Simon M, Lima GS, Gissi DS, Almeida CC, Souza G, Marques A (2021) High-throughput genomic data reveal complex phylogenetic relationships in Stylosanthes Sw (Leguminosae). Front Genet 12:727314
doi: 10.3389/fgene.2021.727314
Silvestri MC, Ortiz AM, Lavia GI (2014) rDNA loci and heterochromatin positions support a distinct genome type for ‘x = 9 species’ of section Arachis (Arachis, Leguminosae). Plant Syst Evol 301:555–562
doi: 10.1007/s00606-014-1092-y
Smartt J, Gregory WC, Gregory MP (1978) The genomes of Arachis hypogaea. 1. Cytogenetic studies of putative genome donors. Euphytica 27:665–675
doi: 10.1007/BF00023701
Stalker HT (1991) A new species-section Arachis of peanuts with D genome. Am J Bot 78:630–637
doi: 10.1002/j.1537-2197.1991.tb12587.x
Stalker HT, Dhesi JS, Parry DC, Hahn JH (1991) Cytological and interfertility relationships of Arachis section Arachis. Am J Bot 78:238–246
doi: 10.1002/j.1537-2197.1991.tb15751.x
Staton SE, Burke JM (2015) Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. BMC Genomics 16:623
pubmed: 26290182
pmcid: 4546089
doi: 10.1186/s12864-015-1830-8
Ugarkovic D, Plohl M (2002) Variation in satellite DNA profiles-causes and effects. EMBO J 2:5955–5959
doi: 10.1093/emboj/cdf612
Usai G, Mascagni F, Natali L, Giordani T, Cavallini A (2017) Comparative genome-wide analysis of repetitive DNA in the genus Populus L. Tree Genet Genomes 13:96
doi: 10.1007/s11295-017-1181-5
Vaio M, Mazzella C, Porro V, Speranza P, López-Carro B, Estramil E, Folle GA (2007) Nuclear DNA content in allopolyploid species and synthetic hybrids in the grass genus Paspalum. Plant Syst Evol 265:109–121
doi: 10.1007/s00606-006-0506-x
Valls JFM, Simpson CE (2005) New species of Arachis from Brazil, Paraguay, and Bolivia. Bonplandia 14:35–64
doi: 10.30972/bon.141-21387
Valls JFM, Simpson CE (2017) A new species of Arachis (Fabaceae) from Mato Grosso, Brazil, related to Arachis matiensis. Bonplandia 26:143–149
doi: 10.30972/bon.2622575
Valls JFM, Da Costa LC, Custodio AR (2013) A novel trifoliolate species of Arachis (Fabaceae) and further comments on the taxonomic section Trierectoides. Bonplandia 22:91–97
doi: 10.30972/bon.2211257
Vitales D, Garcia S, Dodsworth S (2020) Reconstructing phylogenetic relationships based on repeat sequence similarities. Mol Phylogenet Evol 147:106766
pubmed: 32119996
doi: 10.1016/j.ympev.2020.106766
Wang J, Li Y, Li C, Yan C, Zhao X, Yuan C, Sun Q, Shi C, Shan S (2019) Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny. BMC Plant Biol 19:1–18
doi: 10.1186/s12870-018-1600-2
Weiss-Schneeweiss H, Leitch AR, McCann J, Jang TS, Macas J (2015) Employing next generation sequencing to explore the repeat landscape of the plant genome. Next generation sequencing in plant systematics. Regnum Veget 157:155–179
Woo TH, Hong TH, Kim SS, Chung WH, Kang HJ, Kim CB, Seo JM (2007) Repeatome: a database for repeat element comparative analysis in human and chimpanzee. Genomics Inform 5:179–187
Yin D, Wang Y, Zhang X, Ma X, He X, Zhang J (2017) Development of chloroplast genome resources for peanut (Arachis hypogaea L.) and other species of Arachis. Sci Rep 7:1–11
doi: 10.1038/s41598-016-0028-x
Zhang QJ, Gao LZ (2017) Rapid and recent evolution of LTR retrotransposons drives rice genome evolution during the speciation of AA-genome Oryza species. G3: Genes Genom Genet 7:1875–1885
doi: 10.1534/g3.116.037572
Zhang L, Xu C, Yu W (2012) Cloning and characterization of chromosomal markers from a Cot-1 library of peanut (Arachis hypogaea L.). Cytogenet Genome Res 137:31–41
pubmed: 22797674
doi: 10.1159/000339455
Zhang L, Yang X, Tian L, Chen L, Yu W (2016) Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. New Phytol 211:1424–1439
pubmed: 27176118
doi: 10.1111/nph.13999