Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

Abstract

Background Saussurea is one of the most species-rich genera in the Cardueae, Asteraceae. There are approximately 40 Saussurea species distributed in Korea, with nearly 40% of them endemics. Infrageneric relationships remain uncertain due to insufficient resolutions and low statistical support. In this study, we sequenced the plastid genomes of five Korean endemic Saussurea (S. albifolia, S. calcicola, S. diamantica, S. grandicapitula, and S. seoulensis), and comparative analyses including two other endemics (S. chabyoungsanica and S. polylepis) were conducted. Results The plastomes of Korean endemics were highly conserved in gene content, order, and numbers. Exceptionally, S. diamantica had mitochondrial DNA sequences including two tRNAs in SSC region. There were no significant differences of the type and numbers of SSRs among the seven Korean endemics except in S. seoulensis. Nine mutation hotspots with high nucleotide diversity value (Pi > 0.0033) were identified, and phylogenetic analysis suggested that those Korean endemic species most likely evolved several times from diverse lineages within the genus. Moreover, molecular dating estimated that the Korean endemic species diverged since the late Miocene. Conclusions This study provides insight into understanding the plastome evolution and evolutionary relationships of highly complex species of Saussurea in Korean peninsula.

Comparative plastome analysis and taxonomic classification of snow lotus species (Saussurea, Asteraceae) in Central Asia and Southern Siberia

“…The IRb/SSC and IRa/LSC boundary shifts between the species commonly included the ycf 1 and rps 19 pseudogenes, respectively. Overall, our results demonstrated that the conservation pattern of plastomes is similar to those of other Saussurea species (Zhang et al 2019 ; Yun and Kim 2022 ).…”

“…Many studies have reported the use of chloroplast SSR markers with high polymorphisms in Saussurea (Shen et al 2020 ; Yun and Kim 2022 ). In previous studies, the genetic variability in snow lotus species has been investigated using genetic markers of the nuclear genome (Yuan et al 2009 ; Wei et al 2017 ; Nyamgerel et al 2023 ), but they revealed lower genetic diversity.…”

“…Genes with a Ka/Ks > 1 ratio were considered under positive selection, and genes with a Ka/Ks ratio < 1 were considered under purifying selection (Yang and Bielawski 2000 ). Most protein-coding genes in Saussurea are under purifying selection (Zhang et al 2019 ; Yun and Kim 2022 ). Among the snow lotus species, three genes were found to be under positive selection (Fig.…”

High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile (Matricaria recutita) and Roman Chamomile (Chamaemelum nobile)

“…There is limited evidence of DNA transfer between organellar genomes within the Asteraceae family reported in the literature. BLAST search results indicated that the inserted sequences showed a high degree of similarity to mitochondrial DNA sequences from Chrysanthemum , Diplostephium , Lactuca , Helianthus , and Paraprenanthes [ 42 ]. In this study, we conducted an analysis of the homologous sequences between the mitogenomes and plastomes of two chamomile species.…”

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

“…The pairwise sequence divergence was calculated based on the Kimura 2-parameter method ( Kimura, 1980 ) using MEGA11 ( Tamura et al., 2021 ). According to earlier studies, we sequenced the entire plastome (e.g., Kim et al., 2019 ; Cho et al., 2020 ; Yang et al., 2021 ; Yun and Kim, 2022 ). An Illumina paired-end (PE) genomic library was constructed and sequenced using the Illumina HiSeq platform (Illumina, Inc., San Diego, CA, USA) at Macrogen Corporation (Seoul, Korea).…”