Abstract
The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae (P. lunatus) and Glycininae (Amphicarpaea edgeworthii) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus. We also reconstructed the chromosome number reduction in S. suberectus. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.
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Data availability
All data generated or analysed during this study are included as supplementary materials.
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Abbreviations
- 8HQ:
-
8-Hydroxyquinoline
- ACK:
-
Ancestral Crucifer Karyotype
- Ae:
-
Amphicarpaea edgeworthii chromosome
- ALK:
-
Ancestral Legume Karyotype
- APhsK:
-
Ancestral Phaseolus Karyotype
- APK:
-
Ancestral Phaseoleae Karyotype
- APnK:
-
Ancestral Phaseolinae Karyotype
- BACs:
-
Bacterial artificial chromosomes
- DAPI:
-
4’,6-diamidino-2-phenylindole
- DSB:
-
Double-strand break
- FISH:
-
Fluorescence in situ hybridization
- GB:
-
Genomic blocks
- LCT:
-
Legume-common tetraploidization
- Lp:
-
Lablab purpureus chromosome
- LTR:
-
Long terminal repeats
- Ma:
-
Macroptilium atropurpureum chromosome
- Mt:
-
Medicago truncatula chromosome
- Mya:
-
Million years ago
- Oligo:
-
Oligonucleotide
- Pl:
-
Phaseolus lunatus chromosome
- Pv:
-
Phaseolus vulgaris chromosome
- satDNA:
-
Satellite DNA
- Ss:
-
Spatholobus suberectus chromosome
- Vu:
-
Vigna unguiculata chromosome
- WGD:
-
Whole genome duplication
- WGT:
-
Whole genome triplication
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Acknowledgements
We thank Embrapa Meio-Norte (Teresina, Piauí, Brazil), Embrapa Cenargen (Brasília, Distrito Federal, Brazil), CIAT (International Center for Tropical Agriculture), and Prof. Marcelo Guerra (UFPE) for providing the V. unguiculata, P. vulgaris, M. atropurpureum, and L. purpureus seeds, respectively. We thank Ingo Schubert (IPK) and André Marques (MPIPZ) for the early critical review of the manuscript. We also thank CAPES (Coordenação de Pessoal de Nível Superior, Finance Code 001), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), and FACEPE (Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco) for their financial support.
Funding
This work was supported by CAPES (Coordenação de Pessoal de Nível Superior, Finance Code 001), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, grant nos. 310804/2017–5 and 313944/2020–2), and FACEPE (Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, grant nos. IBPG-1520–2.03/18 and APQ-0409–2.02/16).
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C.M.: conducted the genome comparisons, defined the blocks, performed the oligo-FISH painting experiments with M. atropurpureum and L. purpureus, constructed the images, and wrote the original draft of the manuscript. L.V.M: established the oligo-painting probes, performed the oligo-FISH in P. vulgaris and V. unguiculata, constructed the oligo-FISH images, and helped write the manuscript. F.O.B: provided the resources for this research and discussed the data. A.C.B.V: co-supervised the experiments and contributed to the data analyses and discussion. A.P.H: conceptualized and supervised the experiments and provided resources for this research. All authors reviewed the manuscript.
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Key message
We developed a useful genomic block system and proposed the ancestral Phaseoleae karyotype based on available genome assemblies of legume crops. These tools enabled the reconstruction of the main chromosomal rearrangements responsible for genome reshuffling among the diploid taxa investigated. The analyses revealed centromere repositioning in all but one chromosome within the tribe, despite the chromosome number conservation.
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Supplementary file14
Supplementary Figure 1. Dot plot of genome comparison between P. vulgaris and V. unguiculata, with each GB colour based on the APK. Corresponding chromosomes are distributed according to the dot plot order. Dashed lines indicate the centromere positions in the respective GBs. (PNG 360 kb)
Supplementary file15
Supplementary Figure 2. Dot plot of genome comparisons between P. vulgaris and P. lunatus, with each GB colour based on the APK. Corresponding chromosomes are distributed according to the dot plot order. Dashed lines indicate the centromere positions in the respective GBs. (PNG 335 kb)
Supplementary file16
Supplementary Figure 3. Dot plot of genome comparison between P. vulgaris and A. edgeworthii with each GB colour based on the APK. Corresponding chromosomes are distributed according to the dot plot order. (PNG 300 kb)
Supplementary file17
Supplementary Figure 4. Dot plot of genome comparison between P. vulgaris and S. suberectus with each GB colour based on the APK. Corresponding chromosomes are distributed according to the dot plot order. (PNG 271 kb)
Supplementary file18
Supplementary Figure 5. Dot plot of genome comparison between P. vulgaris and M. truncatula with each GB colour based on the APK. Corresponding chromosomes are distributed according to the dot plot order. (PNG 260 kb)
Supplementary file19
Supplementary Figure 6. Schematic representation of the most conserved GB associations of the A. edgeworthii (Ae) karyotype as inferred from comparison with the APK. Despite extensive genome reshuffling, the main GB associations involved in the formation of each Ae chromosome are indicated by dotted lines in the corresponding APK chromosome colours. (PNG 174 kb)
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Montenegro, C., do Vale Martins, L., Bustamante, F.d.O. et al. Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae. Chromosome Res 30, 477–492 (2022). https://doi.org/10.1007/s10577-022-09702-8
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DOI: https://doi.org/10.1007/s10577-022-09702-8