RT Journal Article
SR Electronic
T1 Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.06.455448
DO 10.1101/2021.08.06.455448
A1 Claudio Montenegro
A1 Lívia do Vale Martins
A1 Fernanda de Oliveira Bustamante
A1 Ana Christina Brasileiro-Vidal
A1 Andrea Pedrosa-Harand
YR 2021
UL http://biorxiv.org/content/early/2021/08/07/2021.08.06.455448.abstract
AB The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicated the preservation of large genomic blocks in legumes. However, the chromosome dynamics along its evolution was not investigated in the tribe. We conducted a comparative genomic analysis using CoGe Synmap platform to define a useful genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes (n = 11), then searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus, n = 11) and Glycininae (Amphicarpaea edgeworthii, n = 11 and Spatholobus suberectus, n = 9) subtribes, and in the outgroup (Medicago truncaluta, n = 8). To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of the non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureusi, n = 11). We inferred the APK with n = 11, 22 GBs (A to V) and 60 sub-GBs. We hypothesized that the main rearrangements within Phaseolinae involved nine APK chromosomes, with extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. We demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstructed the main events responsible for the chromosome number reduction. The development of the GB system and the proposed APK provide useful tools for future comparative genomic analyses of legume species.Significance statement We developed a genomic block system and proposed an Ancestral Phaseoleae Karyotype based on available genome assemblies of these legume crops. These tools enabled to reconstruct the main chromosomal rearrangements responsible for the genome reshuffling among the diploid investigated taxa. The analyses also revealed centromere repositioning for all chromosomes, despite conservation of chromosome number.Competing Interest StatementThe authors have declared no competing interest.