Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 10; p. 1449
• Main Authors: Ruang-Areerate, Panthita, Naktang, Chaiwat, Kongkachana, Wasitthee, Sangsrakru, Duangjai, Narong, Nattapol, Maknual, Chatree, Pravinvongvuthi, Tamanai, Promchoo, Waratthaya, Yamprasai, Suchart, Tangphatsornruang, Sithichoke, Pootakham, Wirulda
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.10.2022; MDPI
• Subjects: Climate change; Coasts; Genetic analysis; Genetic diversity; Genomes; Genomics; Heterozygosity; mangrove; Mangrove swamps; Mangroves; Nucleotide sequence; Phylogeny; Population; Population genetics; Population structure; Rhizophora apiculata; Rhizophoraceae; Single-nucleotide polymorphism; Software; Subpopulations; whole-genome; Gulf of Thailand; China; Andaman Sea; Malaysia; Thailand; Indonesia; Bangkok Thailand; genetic diversity; SNP; population structure; whole-genome; Rhizophoraceae; mangrove; Rhizophora apiculata
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11101449

Rhizophora apiculata is one of the most widespread and economically important mangrove trees in the Indo-West Pacific region. Knowledge of the genetic variation of R. apiculata in Thailand is limited. Here, we generated a whole-genome sequence of R. apiculata using the 10× Genomics technology. R. apiculata genome assembly was 230.47 Mb. Based on its genome, 2640 loci of high-quality biallelic SNPs were identified from 82 R. apiculata accessions collected from 17 natural mangrove forests in Thailand to assess the genetic diversity and population structure among them. A moderate level of genetic diversity of R. apiculata was observed. The average observed heterozygosity (Ho = 0.48) was higher than the average expected heterozygosity (He = 0.36). Two subpopulations were observed and confirmed from three approaches: population structure, PCA, and phylogenetic analyses. They corresponded to the Gulf of Thailand and the Andaman Sea separated by the Malay Peninsula. AMOVA analyses indicated that genetic variation was attributable to 76.22% within populations and 23.78% among populations. A high level of genetic differentiation between the two subpopulations (FST = 0.24, p < 0.001) was observed. This study evaluated the genetic diversity and population structure of R. apiculata, providing useful information for sustainable mangrove management in Thailand.