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 2022
UL http://biorxiv.org/content/early/2022/01/10/2021.08.06.455448.abstract
AB The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicate the preservation of large genomic blocks among legumes, however, the chromosome dynamics during Phaseoleae evolution has not been investigated yet. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes. We searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus) and Glycininae subtribes (Amphicarpaea edgeworthii and Spatholobus suberectus), and in the Medicago truncaluta outgroup. To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of two non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureus). We inferred the APK with n = 11 and 19 GBs (A to S). We hypothesized five chromosome fusions that reduced the ancestral legume karyotype with n = 16 to n = 11 in APK. Furthermore, we identified the main rearrangements within Phaseolinae and observed an extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. Additionally, we demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstruct the main events that lead the chromosome number reduction. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.Competing Interest StatementThe authors have declared no competing interest.