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Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand
SIMPLE SUMMARY: In order to examine the genetic diversity and population structure of the Rhizophora mucronata population in Thailand, we utilized 10× Genomics technology to obtain a comprehensive whole-genome sequence, and restriction site associated DNA sequencing (RAD-seq) to genotype the populat...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10044974/ https://www.ncbi.nlm.nih.gov/pubmed/36979175 http://dx.doi.org/10.3390/biology12030484 |
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author | Naktang, Chaiwat Khanbo, Supaporn Yundaeng, Chutintorn U-thoomporn, Sonicha Kongkachana, Wasitthee Jiumjamrassil, Darunee Maknual, Chatree Wanthongchai, Poonsri Tangphatsornruang, Sithichoke Pootakham, Wirulda |
author_facet | Naktang, Chaiwat Khanbo, Supaporn Yundaeng, Chutintorn U-thoomporn, Sonicha Kongkachana, Wasitthee Jiumjamrassil, Darunee Maknual, Chatree Wanthongchai, Poonsri Tangphatsornruang, Sithichoke Pootakham, Wirulda |
author_sort | Naktang, Chaiwat |
collection | PubMed |
description | SIMPLE SUMMARY: In order to examine the genetic diversity and population structure of the Rhizophora mucronata population in Thailand, we utilized 10× Genomics technology to obtain a comprehensive whole-genome sequence, and restriction site associated DNA sequencing (RAD-seq) to genotype the population. Using SNPs discovered from the R. mucronata genome sequence, we detected moderate levels of genetic diversity and differentiation across 80 R. mucronata accessions collected from the coastal regions of Thailand. Both population structure and principal component analysis (PCA) converged on a clustering of two subpopulations. However, the results of two genetic groups did not correspond to the Gulf of Thailand or the Andaman Sea. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. ABSTRACT: Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (F(ST) = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand. |
format | Online Article Text |
id | pubmed-10044974 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-100449742023-03-29 Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand Naktang, Chaiwat Khanbo, Supaporn Yundaeng, Chutintorn U-thoomporn, Sonicha Kongkachana, Wasitthee Jiumjamrassil, Darunee Maknual, Chatree Wanthongchai, Poonsri Tangphatsornruang, Sithichoke Pootakham, Wirulda Biology (Basel) Article SIMPLE SUMMARY: In order to examine the genetic diversity and population structure of the Rhizophora mucronata population in Thailand, we utilized 10× Genomics technology to obtain a comprehensive whole-genome sequence, and restriction site associated DNA sequencing (RAD-seq) to genotype the population. Using SNPs discovered from the R. mucronata genome sequence, we detected moderate levels of genetic diversity and differentiation across 80 R. mucronata accessions collected from the coastal regions of Thailand. Both population structure and principal component analysis (PCA) converged on a clustering of two subpopulations. However, the results of two genetic groups did not correspond to the Gulf of Thailand or the Andaman Sea. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. ABSTRACT: Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (F(ST) = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand. MDPI 2023-03-21 /pmc/articles/PMC10044974/ /pubmed/36979175 http://dx.doi.org/10.3390/biology12030484 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Naktang, Chaiwat Khanbo, Supaporn Yundaeng, Chutintorn U-thoomporn, Sonicha Kongkachana, Wasitthee Jiumjamrassil, Darunee Maknual, Chatree Wanthongchai, Poonsri Tangphatsornruang, Sithichoke Pootakham, Wirulda Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title | Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title_full | Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title_fullStr | Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title_full_unstemmed | Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title_short | Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand |
title_sort | assessment of the genetic diversity and population structure of rhizophora mucronata along coastal areas in thailand |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10044974/ https://www.ncbi.nlm.nih.gov/pubmed/36979175 http://dx.doi.org/10.3390/biology12030484 |
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