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

SIMPLE SUMMARY: We utilized the 10× Genomics technology to obtain a reference whole-genome sequence for assessing the genetic diversity and population structure of Rhizophora apiculata in Thailand. Using SNPs identified from the R. apiculata genome sequence, moderate genetic diversity and high genetic differentiation were observed among 82 R. apiculata accessions collected along the coasts of Thailand. Two subpopulations corresponding to the Gulf of Thailand and the Andaman Sea coasts were clustered and confirmed from three approaches: population structure, PCA, and phylogenetic analyses. The AMOVA result revealed that the percentage of variation within populations (76%) was higher than that among populations (24%). ABSTRACT: 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 (F(ST) = 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.