DOI: 10.5061/dryad.hmgqnk9wr
title: Microsatellites and chloroplast genome sequences of the mangrove (<em>Avicennia marina</em>) from Western Indian Ocean

description: Avicennia marina (Forssk.) Vierh is considered the most widely distributed
 mangrove species and a major constituent of Indo-West Pacific mangroves.
 To understand spatial patterns of genetic diversity in this species, and
 the role of ocean currents and historical events in shaping these
 patterns, we examined population genetic structure, maternal
 phylogeography, and colonization history across the species’ Western
 Indian Ocean range. The data sets include samples from  34
 populations of Kenya, Tanzania, Mozambique, South Africa, Madagascar,
 Mayotte Island, Europa Island, Aldabra atoll, and the Granitic Seychelles
 + outgroups of the Red Sea and Southeast Asia. The data set includes 1,150
 genotyped trees using 18 nuclear microsatellites for conducting population
 genetic analyses, including structure, migrate, barrier, and Bayesian
 origin models. The data set also includes 50 chloroplast sequences (+ 1
 reference) of a nearly complete genome (at least one individual from each
 population) to investigate maternal phylogeography and infer lineage
 origins from a haplotype network.
description: Study area and sampling A total of 1079
 individuals of <em>Avicennia marina</em> from natural mangrove
 forests were collected in 34 locations of the West Indian Ocean (WIO), of
 which 22 were located along the continental eastern African coastline from
 a northernmost site in Lamu, Kenya, to the species' southern range
 limit site of Wavecrest, South Africa. Twelve populations were located on
 Madagascar, Europa Island, Comores (Mayotte Island), the Aldabra atoll,
 and the granitic Seychelles (Mahé, St. Pierre, and Curieuse island). For
 comparative reasons only and as an outgroup in diverse analyses, we
 considered an additional 71 individual trees outside the WIO from a Red
 Sea population (Saudi Arabia), the East Indian Ocean (western Malaysian
 Peninsula), and the East Sea (northern Vietnam). For NGS-based chloroplast
 genome assemblage, a subset of 50 individuals, at least one from each
 population, was used and included 2 individuals from extra WIO sites (Ile
 St Marie in East Madagascar and Nahoon in South Africa) and 9 individuals
 outside the WIO as outgroup region (Red Sea, Bangladesh, southern Malay
 Peninsula, southern and central Vietnam, and Philippines). At each site,
 fresh leaves per tree were collected, dried, and stored in bags with
 silica gel for transport. The distance between sampled individual trees
 ranged between 10 and 100 m, and were taken along transects either
 parallel or perpendicular to the shore or estuarine river. Samples of
 <em>A. marina</em> were made in cooperation with and by local
 researchers that obtained permits from their authorities.
 Microsatellite analysis and data quality Total
 genomic DNA extractions were performed on 20-30 mg leaf material following
 the method as in Triest et al. (2025). We selected 18 microsatellite loci
 out of 38 tested for <em>A. marina</em> (Maguire et al., 2000;
 Geng et al., 2007; Triest et al., 2020) and <em>Avicennia
 alba</em> (Teixeira et al., 2003) based on amplification,
 polymorphism, and data quality. These were Am3<sup>a</sup>,
 Am40<sup>b</sup>, Am49<sup>b</sup>,
 Am81<sup>a</sup>, Aa23<sup>b</sup>,
 Aa67<sup>b</sup>, Avma1<sup>a</sup>,
 Avma2<sup>a</sup>, Avma6<sup>a</sup>,
 Avma8<sup>a</sup>, Avma10<sup>a</sup>,
 Avma14<sup>b</sup>, Avma17<sup>a</sup>,
 AMK3<sup>b</sup>, AMK6<sup>b</sup>,
 AMK10<sup>b</sup>, AMK18<sup>b</sup>, and
 AMK34<sup>b</sup> assembled in two sets (<sup>a,
 b</sup>) of a multiplex polymerase chain reaction (PCR) following
 conditions as detailed in Triest et al. (2025). Geng,
 Q. F., Lian, C. L., Tao, M., Li, Q., and Hogetsus, T. (2007). Isolation
 and characterization of 10 new compound microsatellite markers for a
 mangrove tree species, <em>Avicennia marina</em> (Forsk.)
 Vierh. (Avicenniaceae). <em>Mol. Ecol. Notes</em> 7,
 1208–1210. https://doi.org/10.1111/j.1471-8286.2007.01834.x Maguire, T.L., Edwards, K.J., Saenger, P., and Henry, R. (2000). Characterisation and analysis of microsatellite loci in a mangrove species, <em>Avicennia marina</em> (Forsk.) Vierh. (Avicenniaceae). <em>Theor. Appl. Genet.</em> 101, 279–285. https://doi.org/10.1007/s001220051480 Triest, L., Van der Stocken, T., Akinyi, A.A., Sierens, T., Kairo, J., and Koedam, N. (2020) Channel network structure determines genetic connectivity of landward–seaward <em>Avicennia</em> <em>marina</em> populations in a tropical bay. <em>Ecol. Evol</em>. https://doi.org/10.1002/ece3.6829 Triest, L., Phan Thi Thuy Hang, Luong Quang Doc, Bousquet-Mélou, A., Bich T. N. Do, Sierens, T., Dahdouh-Guebas, F., Koedam, N., and Van der Stocken, T. (2025). Migration history of <em>Avicennia marina</em> populations: a legacy of mangrove expansion on the Sunda Shelf. <em>Frontiers Marine Sc.: Sec. Marine Evolutionary Biology, Biogeography and Species Diversity</em> 12. https://doi.org/10.3389/fmars.2025.1565908 Chloroplast genome assembly, data quality, and alignment The analysis of complete chloroplast sequences through genome skimming followed the detailed protocol as mentioned in Triest et al. (2025). Briefly, genomic DNA extracts were processed for next-generation sequencing (NGS) analysis. Paired-end reads were assembled to a reference (an annotated <em>A. marina</em> chloroplast genome with <em> </em>GenBank accession number MT108381 from Fujian, China, by Li et al., 2020) in Geneious Prime® 2024.0.5 (Biomatters Ltd., Auckland, New Zealand) that perfectly aligned with our reference sample from Kenya (used by Dierckxsens et al., 2017). All mutational steps were recorded, however we encountered ‘heterozygosity’ in many coding genes, due to either two different copies of cpDNA (a biparental plastid inheritance) or caused by nuclear copies of plastid DNA (NUPTs). Therefore, we omitted those ambiguous coding regions and kept only mutational differences of the non-ambiguous cpDNA sequences for further analysis. Ambiguous sequences were detected in 27 genes of the Large Single Copy (LSC) region, including <em>matK, rpoC1, rpoC2, rpoB, psbD, psbC, trnS, atpE, atpB, rbcL, accD, psaI, ycf4, cemA, petA, psbJ, psbL, psbF, psbE, rps11, rpl36, infA, rps8, rpl14, rpl16, rpl2,</em> and <em>rpl23</em>. After removing likely nuclear plastid DNA insertions (NUPTs), 87 mutations were retained in 41 WIO individuals - 45 substitutions (transitions or transversions) and 42 mononucleotide repeats or indels. When including outgroups from the Red Sea and Southeast Asia, a total of 342 mutations were identified: 223 substitutions and 119 mononucleotide repeats or indels. Dierckxsens, N., Mardulyn, P., Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:e18. https://doi.org/10.1093/nar/gkw955. Li, H., Ma, D., Li, J., Wei, M., Zheng, H., and Zhu, X. (2020). Illumina sequencing of complete chloroplast genome of <em>Avicennia marina</em>, a pioneer mangrove species. <em>Mitochondrial DNA B Resour.</em> 5(3), 2131-2132. https://doi.org/10.1080/23802359.2020.1768927 Triest, L., Phan Thi Thuy Hang, Luong Quang Doc, Bousquet-Mélou, A., Bich T. N. Do, Sierens, T., Dahdouh-Guebas, F., Koedam, N., and Van der Stocken, T. (2025). Migration history of <em>Avicennia marina</em> populations: a legacy of mangrove expansion on the Sunda Shelf. <em>Frontiers Marine Sc.: Sec. Marine Evolutionary Biology, Biogeography and Species Diversity</em> 12. https://doi.org/10.3389/fmars.2025.1565908
description: # Microsatellites and chloroplast genome sequences of the mangrove
 (*Avicennia marina*) from Western Indian Ocean Dataset DOI:
 [10.5061/dryad.hmgqnk9wr](10.5061/dryad.hmgqnk9wr) ## Description of the
 data and file structure ### Description of the data and file structure
 **Microsatellite_data_Avicennia_marina_Western_Indiean_Ocean.csv**
 *Avicennia marina* microsatellite scores are provided in GenAlex format: 
 * A1 = number of microsatellite loci * B1 = total number of individuals *
 C1 = total number of populations * D1 to AN1 = number of individuals
 within each of the 37 populations * D2 to AN2 = Locality names * D3 to AN3
 = Population codes * C4 to AL4 = names of 18 microsatellite loci * From
 row 5 onwards: Column A = individual sample codes; B = population codes; C
 to  AL = length of microsatellite allele (biallelic) for each
 microsatellite locus. Zero values are missing values. Population names and
 codes are exactly as in TRIEST et al. 2026 Diversity and Distributions,
 DOI: 10.1111/ddi.70147 (Population genetic structure and colonisation
 history of the widely distributed mangrove *Avicennia marina* across the
 Western Indian Ocean)
 **Avicennia_marina_WIO_chloroplast_sequences_deposit.zip** The chloroplast
 sequences of *Avicennia marina* are in fasta format and include the
 following information in each header, namely &gt; population code,
 publication, number of reads, and mapped against a given reference with
 doi number: &gt;ALD1 Triest et al 2026 Diversity Distributions DOI:
 10.1111/ddi.70147. 80,169 reads mapped to KEN3 (NovoPlasty Nucl acid Res
 doi 10.1093/nar/gkw955) using Geneious. The reference genome from Kenya
 (KEN3_REFERENCE) was additionally uploaded in a GenBank format. ##
 Code/software The microsatellite data can be readily imported into the
 free software GenAlEx 6.5. Peakall, R., and Smouse, P. E. (2012). GenAlEx
 6.5: genetic analysis in Excel. Population genetic software for teaching
 and research – an update. *Bioinform.* 28, 2537–2539. DOI:
 10.1093/bioinformatics/bts460. The fasta files of chloroplast sequences
 can be viewed as a text file and uploaded to platforms of DNA sequences
 for alignment.