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

Abstract

Background DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2n = 28, but dysploid species like Senna tora have also been observed. Objective To understand the dynamics of these TRs and their impact on S. tora dysploidization. Methods We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships. Results Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora, but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea. StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora, was either absent or localized at the subtelomeric or pericentromeric regions in other species. Conclusions These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in “carrying” repeats during genome reshuffling.

Chromosomal dynamics in Senna: comparative PLOP–FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations

“…The presence of StoTR01_86 at the 45S rDNA locus in most Senna species studied, except S. pallida , suggests its involvement in chromosomal rearrangements following the divergence of Senna species from their common ancestor, with the karyotype represented by S. pallida . This process may have led to the correction of error StoTR01_86 which was also observed in S. siamea in the study by Ta et al. (2021) ( Table 1 ).…”

“…They contain a diverse range of important metabolites (alkaloids, anthraquinones, flavonoids, tannins, glycosides, steroids, terpenoids, and saponins) and display a wide range of in vitro and in vivo pharmacological activities (antidiabetic, anti-gonorrhea, antimicrobial, antioxidant, antipyretic, antinociceptive, antidepressant, and anti-inflammatory effects) ( Puri, 2018 ; Kang et al., 2020a ; Oladeji et al., 2021 ). However, the genus Senna presents challenges for cytogenetic studies owing to the diverse morphological and ecological characteristics of its members ( Cordeiro and Felix, 2017 ; Nguyen et al., 2021 ; Ta et al., 2021 ; Waminal et al., 2021 ). Furthermore, Senna exhibits high levels of chromosomal variability with reported chromosome numbers ranging from 14–120 ( Cordeiro and Felix, 2017 ).…”

Genome assembly of the popular Korean soybean cultivar Hwangkeum

“…The weakness or absence of hybridization with satellite repeats to genomic DNA within a genus suggested the rapid divergence of centromeric satellite repeats ( Lee et al 2005 ; Gill et al 2009 ; Ta et al 2021 ), and in the case of rice relatives, novel divergent satellite repeats with low or no sequence similarity with CentO were isolated from several relatives. As genome sequence of G. latifolia ( Liu et al 2018 ), a perennial relative of soybean, is available, we searched CentGm repeats in the G. latifolia genome.…”

Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites

“…Several studies have implicated the involvement of the 45S rDNA array in plant genome rearrangements [ 60 , 66 , 67 , 68 ]. Similarly, we observed the participation of the 45S rDNA array in the rapid evolution of the ACBR_msat20 microsatellite in × Brassicoraphanus 977.…”

“…This observation further demonstrates the role of 45S rDNA in genome reshuffling. Although we have not characterized the sequence of the 45S rDNA in × Brassicoraphanus 977, the ACBR_msat20 microsatellite must have been likely inserted into the 45S rDNA intergenic spacer, as this region is often considered a “logistics hub” of repeats in the genome, hosting different types of repeats into or out of the 45S rDNA intergenic spacer [ 68 , 69 , 70 ]. The 45S rDNA may also facilitate the rapid and efficient concerted expansion and contraction of genomic repeats, as observed in Senna [ 68 ] and the ACBR_msat20 microsatellite in × Brassicoraphanus 977.…”