Microsatellite markers for Saussurea polylepis (Asteraceae), a vulnerable continental island species endemic to Korea

2022

BMC Plant Biol

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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.

Section: Discussionmentioning

confidence: 99%

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

2022

BMC Plant Biol

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“…The total genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen, Carlsbad, California, USA), following the instructions of the manufacturer. PCR was performed using 19 SSR primers ( S1 Table ) as previously developed [ 45 ]. The PCR was conducted with a final reaction volume of 20μL containing 1μL of genomic template DNA, 0.5μL of 10 pmol forward primer with fluorescence dye (HEX or FAM), 0.5μL of 10 pmol reverse primer, 2.5μL (with 2.5mM MgCl 2 ) of PCR buffer, 0.5μL (each 10mM) of dNTPs, 0.1μL (5U/μL) of Taq DNA polymerase (Inclone Biotech, Gyeonggido, Korea), and 14.9μL of distilled water.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and structure of Saussurea polylepis (Asteraceae) on continental islands of Korea: Implications for conservation strategies and management

2021

PLoS ONE

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Saussurea polylepis Nakai is an herbaceous perennial endemic to Korea and is highly restricted to several continental islands in the southwestern part of the Korean Peninsula. Given its very narrow geographical distribution, it is more vulnerable to anthropogenic activities and global climate changes than more widely distributed species. Despite the need for comprehensive genetic information for conservation and management, no such population genetic studies of S. polylepis have been conducted. In this study, genetic diversity and population structure were evaluated for 97 individuals from 5 populations (Gwanmaedo, Gageodo, Hongdo, Heusando, and Uido) using 19 polymorphic microsatellites. The populations were separated by a distance of 20–90 km. We found moderate levels of genetic diversity in S. polylepis (Ho = 0.42, He = 0.43). This may be due to long lifespans, outcrossing, and gene flow, despite its narrow range. High levels of gene flow (Nm = 1.76, mean Fst = 0.09), especially from wind-dispersed seeds, would contribute to low levels of genetic differentiation among populations. However, the small population size and reduced number of individuals in the reproductive phase of S. polylepis can be a major threat leading to inbreeding depression and genetic diversity loss. Bayesian cluster analysis revealed three significant structures at K = 3, consistent with DAPC and UPGMA. It is thought that sea level rise after the last glacial maximum may have acted as a geographical barrier, limiting the gene flow that would lead to distinct population structures. We proposed the Heuksando population, which is the largest island inhabited by S. polylepis, as a source population because of its large population size and high genetic diversity. Four management units (Gwanmaedo, Gageodo, Hongdo-Heuksando, and Uido) were suggested for conservation considering population size, genetic diversity, population structure, unique alleles, and geographical location (e.g., proximity).

Section: Nucleotide Diversity and Selection Pressurementioning

confidence: 99%

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

2022

Preprint

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.