Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy

Abstract

Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7–5,833 bp and 325–2.89 × 106, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.

Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna

“…The chromosomal distribution of StoTR01_86 in S. tora was in total contrast with that observed in the Senna species in this study. Although StoTR01_86 was localized in the pericentromeric regions in all S. tora chromosomes (Waminal et al 2021), it was absent in the pericentromeric region in all currently investigated Senna species but colocalized at all 45S rDNA loci, except in S. siamea, which did not show any StoTR01_86 signal at all (Figs. 2, 3 and 4; Table 2).…”

“…The StoTR02_7_Tel, which is an Arabidopsis-type telomere repeat sequence, was highly amplified in the interstitial regions of S. tora chromosomes in addition to the canonical sites at chromosome termini (Pellerin et al 2019;Waminal et al 2021). Likewise, StoTR05_180 was also mostly colocalized with StoTR02_7_Tel in S. tora in pericentromeric regions but absent in subtelomeric sites.…”

“…S. tora TRs were identified using low-coverage sequences and short-read clustering with TAREAN (Novák et al 2017) in our previous study (Waminal et al 2018a(Waminal et al , 2021. All prelabeled oligonucleotide probes (PLOPs) used in this study are listed in Table 1.…”

“…Out of the eight S. tora TRs (Waminal et al 2021), two were not detected by FISH in all nine Senna species (StoTR03_178 and StoTR04_55), while the other six were either present in all or only a few species (Table 2). StoTR02_7_tel, StoTR05_180, Sto_5S, and Sto_45S_ CDS were detected in all species, whereas StoTR01_86 and StoTR06_159 were observed only in eight and four species, respectively (Fig.…”

“…The predominant chromosome number of the genus Senna is 2n = 28 (Rice et al 2015), but species with descending dysploid karyotypes of 2n = 22-26 have also been identified, such as S. tora with 2n = 26 (Cordeiro and Felix 2018;Pellerin et al 2019). To understand the dysploidization in S. tora, we examined its genome TR composition in our previous work (Waminal et al 2021). We identified eight S. tora TRs, many of which showed unusual chromosomal distributions.…”