Phylogeographic genetic variation of Indoplanorbis exustus (Deshayes, 1834) (Gastropoda: Planorbidae) in South and Southeast Asia.

The freshwater snail Indoplanorbis exustus play an important role as the sole intermediate host of several medically- and economically-important trematodes, especially zoonotic schistosomes and echinostomes, which can infect and cause diseases in livestock and people. This study aims to explore the mitochondrial cytochrome c oxidase subunit 1 sequence variation of I. exustus collected from new geographical areas; 459 specimens of I. exustus were collected from 43 localities in South and Southeast Asia. The 42 haplotypes (Ie1 - Ie42) we detected were classified into haplogroups I - V. Phylogenetic analyses revealed five major clades, A - E, in concordance with all previous studies. Clade E contained two subclades, E1 (haplogroup I) and E2 (haplogroup II). The most widespread genetic group was subclade E1. Clade A, clade B (haplogroup V), and clade C (haplogroup IV) were found only in South Asia, whereas clade D (haplogroup III) was specifically found in Southeast Asia. In Thailand, I. exustus showed high genetic divergence with 21 haplotypes. Several isolates showed significant genetic differences from others with unique haplotype(s). Hence, we confidently conclude our findings support all previous studies that I. exustus is a species complex with at least four major lineages and five haplogroups. Our additional analyses of 35 samples from Sri Lanka showed these were indeed an independent genetic group as previously found, but they can now be classified as a unique group forming subclade E2 (haplogroup II) of I. exustus sensu lato.

Genetic structure and geographical variation of Bithynia siamensis goniomphalos sensu lato (Gastropoda: Bithyniidae), the snail intermediate host of Opisthorchis viverrini sensu lato (Digenea: Opisthorchiidae) in the Lower Mekong Basin revealed by mitochondrial DNA sequences.

The freshwater snail Bithynia siamensis goniomphalos sensu lato is widely distributed in the Lower Mekong Basin where it acts as the first intermediate host of the liver fluke Opisthorchis viverrini, a group 1 carcinogen causing cholangiocarcinoma. This study explores the genetic structure and geographical variation of B. s. goniomphalos from eight previously studied catchments and eight new catchments. These catchments belong to five previously studied catchment systems and one new catchment system (Tonlesap) in the Lower Mekong Basin. Two new catchment systems, Prachin Buri and Bang Pakong from eastern and central Thailand, respectively, were also examined. We collected 289 specimens of B. s. goniomphalos from 15 previously studied localities and 18 new localities in Thailand, Lao PDR (People's Democratic Republic), and Cambodia. The mitochondrial cytochrome c oxidase subunit 1 and 16S ribosomal DNA sequences were used to determine genetic variation. Classification of haplotypes specified 100 at the cox1 locus and 15 at the rrnL locus. Comparison between 16 catchment populations found significant genetic differences (ФST) between all populations. The phylogenetic tree and haplotype network analyses classified B. s. goniomphalos into three evolutionary lineages (lineage I-III). Lineage I contained B. s. goniomphalos from the Mekong, Chi, Mun, Prachin Buri and Bang Pakong catchments in Thailand, including the Nam Ngum catchment in Lao PDR. Lineage II contained all specimens from the Tonlesap catchment, whereas lineage III contained specimens from the Mekong and Sea Bang Heang catchments in Thailand and Lao PDR, respectively. Interestingly, Bithynia siamensis siamensis was placed between lineages I and II of B. s. goniomphalos. This study supports the hypothesis that B. s. goniomphalos is a species complex containing at least three distinct evolutionary lineages in the Lower Mekong Basin, and that comprehensive molecular genetic analyses need to be conducted to further our understanding of the evolutionary and systematic relationships of these Bithynia snail taxa.

Genetic diversity and population structure of blue-crested lizard, Calotes mystaceus Duméril & Bibron, 1837 (Squamata: Agamidae) in Thailand.

The blue-crested lizard, Calotes mystaceus Duméril & Bibron, 1837, is listed as a protected wild animal in Thailand. Its population is likely to be dramatically reduced due to massive hunting in several areas in this country. Basic information on its population genetics is therefore needed to facilitate its conservation. Thus, in this study we investigated the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequence variation of 238 individualC.mystaceus from 42 different geographical localities of the north, west, central, east and northeast regions of Thailand. High genetic diversity and genetic differentiation at the intrapopulation and interpopulation levels was observed.We detected 63 unique haplotypes and 12 common/shared haplotypes. The phylogenetic analysis reveals two major lineages, I and II. These two lineages are separated by mountain ranges, which play an important role as natural barriers blocking gene flow. Our finding reveal at least two cryptic lineages represented in C. mystaceus populations in Thailand. However, a comprehensive investigation of the morphology, biology, ecology and genetic diversity of C. mystaceus in other regions within its area of distribution is needed.

Diversity of the Potential 2-Methylisoborneol-Producing Genotypes in Thai Strains of Planktothricoides (Cyanobacteria)

ABSTRACT The genus Planktothricoides Suda & Watanabe is considered as a 2-methylisoborneol (MIB) producer, affecting water quality and aquatic animal products worldwide. To date, there is limited information about the diversity of this genus from Thailand. In this study, Thai Planktothricoides strains were isolated from fish ponds and reservoirs in North, Northeast and Central regions for morphological examination, phylogenetic analyses based on 16S rRNA, rbcLX and MIB synthase genes as well as GC/MS/MS analyses. The morphological results and the 16S rRNA and rbcLX phylogenies of Thai Planktothricodes strains enabled them to be designated as Planktothricoides raciborskii. Cell dimensions of Thai strains tested were in 1.86 to 5.96 µm length (L), 2.83 to 13.70 µm width (W), and the L/W ratio ranged from 1:6 to 1:1. Among Planktothricoides strains, the 16S rRNA phylogenies demonstrated that three subclades (A, B and C groups) were apparently divided. The similarity of 16S rRNA genes between subclades were 96-98%. From the detection of MIB synthase genes and GC/MS/MS analyses, some strains grouped into A group were considered as MIB-producers. In this study, most Thai Planktothricoides strains belonging to the A group were found in all three regions, while the strains forming the B and C groups were not distributed in the North region. To our knowledge, the present study is the first report investigation and characterization of the potential MIB-producing Planktothricoides from Thailand. Therefore, providing a valuable tool as a model for the early prediction and detection of taste and odor event is necessary.

Quantitative PCR assay for detection and enumeration of ciguatera-causing dinoflagellate Gambierdiscus spp. (Gonyaulacales) in coastal areas of Japan.

In Japan, ciguatera fish poisoning (CFP) has been increasingly reported not only in subtropical areas but also in temperate areas in recent years, causing a serious threat to human health. Ciguatera fish poisoning is caused by the consumption of fish that have accumulated toxins produced by an epiphytic/benthic dinoflagellate, genus Gambierdiscus. Previous studies revealed the existence of five Gambierdiscus species/phylotypes in Japan: Gambierdiscus australes, Gambierdiscus scabrosus, Gambierdiscus sp. type 2, Gambierdiscus sp. type 3, and Gambierdiscus (Fukuyoa) cf. yasumotoi. Among these, G. australes, G. scabrosus, and Gambierdiscus sp. type 3 strains exhibited toxicities in mice, whereas Gambierdiscus sp. type 2 strains did not show any toxicity. Therefore, it is important to monitor the cell abundance and dynamics of these species/phylotypes to identify and characterize CFP outbreaks in Japan. Because it is difficult to differentiate these species/phylotypes by observation under a light microscope, development of a rapid and reliable detection and enumeration method is needed. In this study, a quantitative PCR assay was developed using a TaqMan probe that targets unique SSU rDNA sequences of four Japanese Gambierdiscus species/phylotypes and incorporates normalization with DNA recovery efficiency. First, we constructed standard curves with high linearity (R2=1.00) and high amplification efficiency (≥1.98) using linearized plasmids that contained SSU rDNA of the target species/phylotypes. The detection limits for all primer and probe sets were approximately 10 gene copies. Further, the mean number of SSU rDNA copies per cell of each species/phylotype was determined from single cells in culture and from those in environmental samples using the qPCR assay. Next, the number of cells of each species/phylotype in the mixed samples, which were spiked with cultured cells of the four species/phylotypes, was calculated by division of the total number of rDNA copies of each species/phylotype in each sample by the number of rDNA copies per cell. The numbers of cells of each species/phylotype quantified by qPCR assay were similar to the number of cells of each species/phylotype that were spiked. Finally, the cell densities of the target species/phylotypes were quantified using the qPCR assay in 30 environmental samples collected from Japanese coastal areas. Total cell densities of the four Gambierdiscus species/phylotypes quantified by qPCR assay were similar to those of Gambierdiscus spp. quantified by direct counting under a light microscope. The qPCR assay developed in this study is expected to be a powerful new tool for determining detailed distribution patterns and for monitoring the cell abundance and dynamics of each Japanese Gambierdiscus species/phylotype in the coastal areas of Japan.

Morphology of Gambierdiscus scabrosus sp. nov. (Gonyaulacales): a new epiphytic toxic dinoflagellate from coastal areas of Japan.

A new epiphytic dinoflagellate is described, G ambierdiscus scabrosus sp. nov., from tidal pools and rocky shores along the coastal areas of Japan. Cells are 63.2 ± 5.7 µm in depth, 58.2 ± 5.7 µm in width, and 37.3 ± 3.5 µm in length. The plate formula of G . scabrosus is Po, 4', 0a, 6'', 6c, ?s, 5''', 0p, and 2''''. Morphologically, G . scabrosus resembles G . belizeanus as follows: anterioposteriorly compressed cell shape, narrow 2'''' plate, and areolated surface. Despite this similarity, the cells of G . scabrosus can be distinguishable by the presence of the asymmetric shaped 3'' plate and the rectangular shaped 2' plate.

Quantitative PCR method for enumeration of cells of cryptic species of the toxic marine dinoflagellate Ostreopsis spp. in coastal waters of Japan.

Monitoring of harmful algal bloom (HAB) species in coastal waters is important for assessment of environmental impacts associated with HABs. Co-occurrence of multiple cryptic species such as toxic dinoflagellate Ostreopsis species make reliable microscopic identification difficult, so the employment of molecular tools is often necessary. Here we developed new qPCR method by which cells of cryptic species can be enumerated based on actual gene number of target species. The qPCR assay targets the LSU rDNA of Ostreopsis spp. from Japan. First, we constructed standard curves with a linearized plasmid containing the target rDNA. We then determined the number of rDNA copies per cell of target species from a single cell isolated from environmental samples using the qPCR assay. Differences in the DNA recovery efficiency was calculated by adding exogenous plasmid to a portion of the sample lysate before and after DNA extraction followed by qPCR. Then, the number of cells of each species was calculated by division of the total number of rDNA copies of each species in the samples by the number of rDNA copies per cell. To test our procedure, we determined the total number of rDNA copies using environmental samples containing no target cells but spiked with cultured cells of several species of Ostreopsis. The numbers estimated by the qPCR method closely approximated total numbers of cells added. Finally, the numbers of cells of target species in environmental samples containing cryptic species were enumerated by the qPCR method and the total numbers also closely approximated the microscopy cell counts. We developed a qPCR method that provides accurate enumeration of each cryptic species in environments. This method is expected to be a powerful tool for monitoring the various HAB species that occur as cryptic species in coastal waters.

Genetic diversity and distribution of the ciguatera-causing dinoflagellate Gambierdiscus spp. (Dinophyceae) in coastal areas of Japan.

BACKGROUND: The marine epiphytic dinoflagellate genus Gambierdiscus produce toxins that cause ciguatera fish poisoning (CFP): one of the most significant seafood-borne illnesses associated with fish consumption worldwide. So far, occurrences of CFP incidents in Japan have been mainly reported in subtropical areas. A previous phylogeographic study of Japanese Gambierdiscus revealed the existence of two distinct phylotypes: Gambierdiscus sp. type 1 from subtropical and Gambierdiscus sp. type 2 from temperate areas. However, details of the genetic diversity and distribution for Japanese Gambierdiscus are still unclear, because a comprehensive investigation has not been conducted yet. METHODS/PRINCIPAL FINDING: A total of 248 strains were examined from samples mainly collected from western and southern coastal areas of Japan during 2006-2011. The SSU rDNA, the LSU rDNA D8-D10 and the ITS region were selected as genetic markers and phylogenetic analyses were conducted. The genetic diversity of Japanese Gambierdiscus was high since five species/phylotypes were detected: including two reported phylotypes (Gambierdiscus sp. type 1 and Gambierdiscus sp. type 2), two species of Gambierdiscus (G. australes and G. cf. yasumotoi) and a hitherto unreported phylotype Gambierdiscus sp. type 3. The distributions of type 3 and G. cf. yasumotoi were restricted to the temperate and the subtropical area, respectively. On the other hand, type 1, type 2 and G. australes occurred from the subtropical to the temperate area, with a tendency that type 1 and G. australes were dominant in the subtropical area, whereas type 2 was dominant in the temperate area. By using mouse bioassay, type 1, type 3 and G. australes exhibited mouse toxicities. CONCLUSIONS/SIGNIFICANCE: This study revealed a surprising diversity of Japanese Gambierdiscus and the distribution of five species/phylotypes displayed clear geographical patterns in Japanese coastal areas. The SSU rDNA and the LSU rDNA D8-D10 as genetic markers are recommended for further use.

Phylogeography of ostreopsis along west Pacific coast, with special reference to a novel clade from Japan.

BACKGROUND: A dinoflagellate genus Ostreopsis is known as a potential producer of Palytoxin derivatives. Palytoxin is the most potent non-proteinaceous compound reported so far. There has been a growing number of reports on palytoxin-like poisonings in southern areas of Japan; however, the distribution of Ostreopsis has not been investigated so far. Morphological plasticity of Ostreopsis makes reliable microscopic identification difficult so the employment of molecular tools was desirable. METHODS/PRINCIPAL FINDING: In total 223 clones were examined from samples mainly collected from southern areas of Japan. The D8-D10 region of the nuclear large subunit rDNA (D8-D10) was selected as a genetic marker and phylogenetic analyses were conducted. Although most of the clones were unable to be identified, there potentially 8 putative species established during this study. Among them, Ostreopsis sp. 1-5 did not belong to any known clade, and each of them formed its own clade. The dominant species was Ostreopsis sp. 1, which accounted for more than half of the clones and which was highly toxic and only distributed along the Japanese coast. Comparisons between the D8-D10 and the Internal Transcribed Spacer (ITS) region of the nuclear rDNA, which has widely been used for phylogenetic/phylogeographic studies in Ostreopsis, revealed that the D8-D10 was less variable than the ITS, making consistent and reliable phylogenetic reconstruction possible. CONCLUSIONS/SIGNIFICANCE: This study unveiled a surprisingly diverse and widespread distribution of Japanese Ostreopsis. Further study will be required to better understand the phylogeography of the genus. Our results posed the urgent need for the development of the early detection/warning systems for Ostreopsis, particularly for the widely distributed and strongly toxic Ostreopsis sp. 1. The D8-D10 marker will be suitable for these purposes.