DNA Content Estimation in the Genus Salvia

Abstract

Salvia is a genetically diverse genus in the Lamiaceae family, with hundreds of species distributed globally. With base chromosome numbers ranging from 6 to 19 and ploidy levels ranging from diploid to octoploid, the genus has been proposed to be subdivided based on molecular data rather than morphology. However, little is known about total DNA content across the genus. The DNA content of 141 Salvia genotypes were analyzed using flow cytometry. Samples of Salvia were stained with propidium iodide and compared with the internal standards Pisum sativum ‘Ctirad’ and Solanum lycopersicum ‘Stupické’ to generate estimations of DNA content. Holoploid 2C genome sizes of the analyzed Salvia ranged from 0.63 pg to 6.12 pg. DNA content showed a wide distribution across chromosome number, ploidy, and clade. The wide distribution of DNA content across the genus further indicates the diversity of Salvia and may be useful for future breeding efforts.

Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α‐linolenic (ω‐3) content in S. hispanica seeds

“…The size of S. hispanica pseudo‐chromosomes obtained through Hi‐C scaffolding ranged from 40 to 58 Mb with spanned gaps of 491 to 741 bp (Table S5). The L90 = 6 (Figure S4) is consistent with the chromosome number reported by Maynard and Ruter (2022). The best k‐mer distribution model was obtained for k = 19 and supported diploidy with 0.24% heterozygosity and 5.28% duplicated regions (Figure S5).…”

“…The best k‐mer distribution model was obtained for k = 19 and supported diploidy with 0.24% heterozygosity and 5.28% duplicated regions (Figure S5). Analysis of k‐mer frequencies estimated a haploid genome size of 466 Mbp, consistent with the size of 460 Mbp reported by Maynard and Ruter (2022).…”

“…Early research determined chia's somatic chromosome number and DNA content (2n = 2x = 12, C ‐value = 0.93 ± 0.016 pg, genome size = ∼460 Mb) (Estilai et al., 1990; Haque, 1980; Maynard & Ruter, 2022). In recent years, several studies have provided multi‐tissue transcriptomes for S. hispanica in order to identify genes involved in secondary metabolite and oil biosynthesis (Gupta et al., 2021; Peláez et al., 2019; Sreedhar et al., 2015; Wimberley et al., 2020).…”

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

“…Moreover, intra-and interspecific variations in genome size might reflect different evolutionary processes during speciation [64,66]. The average genome size of S. officinalis is small (1C = 479.22-572.17 Mbp), and it roughly corresponds to that of S. sclarea (1C = 567.24-655.26 Mbp) [67][68][69]. At the same time, between these species, we revealed differences in genome proportions of the total content of retrotransposons, in ratio between Ty3-Gypsy/Ty1-Copia elements, in proportion to other retroelements, including SIRE, Angela, non-chromovirus Tat-Retand, non-chromovirus Athila, chromovirus Tekay, and also the total amount of DNA transposons.…”

“…For S. officinalis and S. sclarea, genome DNA low-coverage sequencing was performed at the Beijing Genomics Institute (BGISeq platform) (Shenzhen, Guangdong, China) according to the NGS protocol for generating 5 million of paired-end reads of 150 bp in length, which was at least 1.1-1.5x of the coverage of these Salvia genomes [67][68][69]. The raw sequencing data for S. officinalis and S. sclarea are available in the NCBI (National Center for Biotechnology Information) BioProject database under accession number PRJNA861221 (https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB11837398/overview).…”