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Naktang C, Khanbo S, Yundaeng C, U-thoomporn S, Kongkachana W, Jiumjamrassil D, Maknual C, Wanthongchai P, Tangphatsornruang S, Pootakham W. Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand. BIOLOGY 2023; 12:484. [PMID: 36979175 PMCID: PMC10044974 DOI: 10.3390/biology12030484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023]
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 (FST = 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.
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Affiliation(s)
- Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Supaporn Khanbo
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chutintorn Yundaeng
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sonicha U-thoomporn
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Darunee Jiumjamrassil
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Poonsri Wanthongchai
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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Pootakham W, Sonthirod C, Naktang C, Yundaeng C, Yoocha T, Kongkachana W, Sangsrakru D, Somta P, Tangphatsornruang S. Genome assemblies of Vigna reflexo-pilosa (créole bean) and its progenitors, Vigna hirtella and Vigna trinervia, revealed homoeolog expression bias and expression-level dominance in the allotetraploid. Gigascience 2022; 12:giad050. [PMID: 37470496 PMCID: PMC10357499 DOI: 10.1093/gigascience/giad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Vigna reflexo-pilosa (créole bean) is a wild legume belonging to the subgenus Ceratoropis and is widely distributed in Asia. Créole bean is the only tetraploid species in the genus Vigna, and it has been shown to derive from the hybridization of Vigna hirtella and Vigna trinervia. In this study, we combined the long-read PacBio technology with the chromatin contact mapping (Hi-C) technique to obtain a chromosome-level assembly of V. reflexo-pilosa. The final assembly contained 998,724,903 bases with an N50 length of 42,545,650 bases. Our gene prediction recovered 99.4% of the highly conserved orthologs based on the BUSCO analysis. To investigate homoeolog expression bias and expression level dominance in the tetraploid, we also sequenced and assembled the genomes of its progenitors. Overall, the majority of the homoeolog pairs (72.9%) displayed no expression bias, and among those that exhibited biased expression, 16.3% showed unbalanced homoeolog expression bias toward the V. trinervia subgenome. Moreover, 41.2% and 36.2% of the expressed gene pairs exhibited transgressive expression and expression level dominance, respectively. Interestingly, the genome-wide expression level dominance in the tetraploid was biased toward the V. trinervia subgenome. The analysis of methylation patterns also revealed that the average methylation levels in coding regions were higher in the V. hirtella subgenome than those in the V. trinervia subgenome. The genomic/transcriptomic resources for these three species are useful not only for the development of elite cultivars in Vigna breeding programs but also to researchers studying comparative genomics and investigating genomic/epigenomic changes following polyploid events.
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Affiliation(s)
- Wirulda Pootakham
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chutintorn Yundaeng
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Thippawan Yoocha
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Duangjai Sangsrakru
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency (NSTDA), National Center for the Genetic Engineering and Biotechnology (BIOTEC), 111 Thailand Science Park, Pathum Thani 12120, Thailand
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Pootakham W, Yoocha T, Jomchai N, Kongkachana W, Naktang C, Sonthirod C, Chowpongpang S, Aumpuchin P, Tangphatsornruang S. A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand. BIOLOGY 2022; 11:biology11101492. [PMID: 36290398 PMCID: PMC9598492 DOI: 10.3390/biology11101492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022]
Abstract
Mitragyna speciosa (Kratom) is a tropical narcotic plant native to Southeast Asia with unique pharmacological properties. Here, we report the first chromosome-scale assembly of the M. speciosa genome. We employed PacBio sequencing to obtain a preliminary assembly, which was subsequently scaffolded using the chromatin contact mapping technique (Hi-C) into 22 pseudomolecules. The final assembly was 692 Mb with a scaffold N50 of 26 Mb. We annotated a total of 39,708 protein-coding genes, and our gene predictions recovered 98.4% of the highly conserved orthologs based on the BUSCO analysis. The phylogenetic analysis revealed that M. speciosa diverged from the last common ancestors of Coffea arabica and Coffea canephora approximately 47.6 million years ago. Our analysis of the sequence divergence at fourfold-degenerate sites from orthologous gene pairs provided evidence supporting a genome-wide duplication in M. speciosa, agreeing with the report that members of the genus Mitragyna are tetraploid. The STRUCTURE and principal component analyses demonstrated that the 85 M. speciosa accessions included in this study were an admixture of two subpopulations. The availability of our high-quality chromosome-level genome assembly and the transcriptomic resources will be useful for future studies on the alkaloid biosynthesis pathway, as well as comparative phylogenetic studies in Mitragyna and related species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Srimek Chowpongpang
- National Biobank of Thailand, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Panyavut Aumpuchin
- National Biobank of Thailand, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Correspondence:
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Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand. BIOLOGY 2022; 11:biology11101449. [PMID: 36290353 PMCID: PMC9598538 DOI: 10.3390/biology11101449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
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 (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.
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