Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae)

Abstract

The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20–24% (Class I) and about 2–2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5–10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.

Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 21 species

“…Conversely, 5S rDNA FISH signal sites in previous research ranged from 1 to 71 (Rodríguez-González et al 2023). Quite of species conserve 5S rDNA, including only two stable chromosomes with two 5S rDNA signal sites (Zhang et al 2016, Moraes et al 2022, Yurkevich et al 2022, Alexandrov et al 2022, Khensuwan et al 2023). Nevertheless, a few species occupy visible 5S rDNA FISH signals, including the numbers of both major and visible dispersed sites.…”

“…Franco (Amarasinghe and Carlson 1988), or in the chromosome proximal position from Brassica rapa L. (Campomayor et al 2021), even as far away the chromosome from Hedysarum setigerum Turcz. (Yurkevich et al 2022), and P. cerasus (Wang et al 2022).…”

“…species of Cucurbitaceae (Li et al 2016); in cultural/wild Hippophaë rhamnoides ssp. sinensis and three Hippophaë rhamnoides L. cultivars of Elaeagnaceae (Luo et al 2022a); in Fabaceae of six Hedysarum L. species (Yurkevich et al 2022); in Juglans regia L. and Juglans sigillata Dode (Luo and Chen) of Juglandaceae; in four Glechoma L. species of Lamiaceae (Jang et al 2016); in three Bletilla Rchb. f. species of Orchidaceae (Huan et al 2022); in three Zea L. species of Poaceae (Han et al 2003); in four Citrus L. species of Rutaceae (He et al 2020), Zanthoxylum bungeanum Maxim.…”

Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae)

“…At the same time, the comprehensive molecular cytogenetic characterization of most Salvia species is still required to investigate the chromosomal evolution within the genus. It was shown for other plant species that such studies usually include FISH-based chromosome mapping of various molecular markers, e.g., 45S rDNA, 5S rDNA and other tandem repeats (satellite DNA families) [29][30][31][32]. However, the chromosome diversity as well as relationships between genomes within the genus Salvia still remain unexplored.…”

“…Such an approach is widely used in comparative repeatome analyses between related species, and it provides new insight into the organization and divergence of their genomes [29,49,50]. Moreover, newly revealed families of satellite DNA (satDNAs) are often used as chromosome markers in comparative molecular cytogenetic studies to assess intra-and interspecific diversity of genomes in various plant taxa [29][30][31][32]50].…”