Data from: Inferences of evolutionary history of a widely distributed mangrove species, Bruguiera gymnorrhiza, in the Indo-West Pacific region

Inference of genetic structure and demographic history is fundamental issue in evolutionary biology. We examined the levels and patterns of genetic variation of a widespread mangrove species in the Indo-West Pacific region, Bruguiera gymnorrhiza, using ten nuclear gene regions. Genetic variation of individual populations covering its distribution range was low, but as the entire species it was comparable to other plant species. Genetic differentiation among the investigated populations was high. They could be divided into two genetic clusters: the West and East clusters of the Malay Peninsula. Our results indicated that these two genetic clusters derived from their ancestral population whose effective size of which was much larger compared to the two extant clusters. The point estimate of speciation time between B. gymnorrhiza and Bruguiera sexangula was two times older than that of divergence time between the two clusters. Migration from the West cluster to the East cluster was much higher than the opposite direction but both estimated migration rates were low. The past Sundaland and/or the present Malay Peninsula are likely to prevent gene flow between the West and East clusters and function as a geographical or land barrier

IMa2_BSvsBG_IS-HKY

IMa2_BSvsBG_IS-HK

STRUCTURE_input

STRUCTURE_inpu

IMa2_BG_K2

IMa2_BG_K

Highly differentiated population structure of a Mangrove species, Bruguiera gymnorhiza (Rhizophoraceae) revealed by one nuclear GapCp and one chloroplast intergenic spacer trnF–trnL

To evaluate the genetic diversity of a mangrove species and clarify the genetic structure of its populations, we studied nucleotide polymorphism in two DNA regions of Bruguiera gymnorhiza collected from the southern islands of Japan, Thailand, Malaysia, Indonesia, Micronesia, and India. The two DNA sequences were the chloroplast (cp) intergenic spacer between trnL and trnF genes (ca. 300 bp), and a part (ca. 550 bp) of the nuclear gene coding for glyceraldehyde-3-phosphate dehydrogenase (GapCp). Little polymorphism was found within each of the three geographical regions, Pacific Ocean, Bay of Bengal and Arabian Sea. Throughout the vast regions eas

Expression patterns of the top five genes encoding TSR domain proteins in <i>Hydra oligactis</i>.

<p>(A) A schematic drawing of a longitudinal cross section of an adult hydra. (B-F) Expression patterns of the top five genes encoding TSR domain proteins in <i>Hydra oligactis</i> by whole mount <i>in situ</i> hybridization. All the genes are expressed in the head region. The accession numbers of the genes were shown on the lower left in each panel.</p

Expression patterns of the genes encoding TSR domain proteins of the A-C groups in the head region of <i>Hydra oligactis</i>.

<p>Among the 10 genes of the A-C groups, six (A- D, G and I) are strongly expressed in the endodermal cells and two (H and J) in the ectodermal cells of the hypostome. The transcripts of XM_002167490 (E) and XM_00215776 (F) were only detected in the tentacles, and not in the hypostome. XM_002160899 (H) was detected in the ectodermal cells of both the hypostome and tentacles. Accession numbers were labeled on the lower left of each panel. The domain structures of the genes were shown on the top of photo panels for each group.</p

Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of <i>Hydra</i>

<div><p>The head region of <i>Hydra</i>, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of <i>Hydra oligactis</i> using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount <i>in situ</i> hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of <i>Hydra oligactis</i>. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of <i>Hydra oligactis</i>.</p></div

Domain structures of <i>Hydra magnipapillata</i> TSR domain proteins.

<p>The domain structures of TSR domain proteins identified in the present study. TSR domains are indicated by red ovals. The accession numbers are from the NCBI nucleotide database.</p

Results of a BLAST homology search of cDNA clones isolated from the SSH library of <i>Hydra oligactis</i>.

<p>Results of a BLAST homology search of cDNA clones isolated from the SSH library of <i>Hydra oligactis</i>.</p