Emiko Oguri

Phylogenetic and biochemical characterization of the oil-producing yeast Lipomyces starkeyi

Lipomyces starkeyi is an oleaginous yeast, and has been classified in four distinct groups, i.e., sensu stricto and custers α, β, and γ. Recently, L. starkeyi clusters α, β, and γ were recognized independent species, Lipomyces mesembrius, Lipomyces doorenjongii, and Lipomyces kockii, respectively. In this study, we investigated phylogenetic relationships within L. starkeyi, including 18 Japanese wild strains, and its related species, based on internal transcribed spacer sequences and evaluated biochemical characters which reflected the phylogenetic tree. Phylogenetic analysis showed that most of Japanese wild strains formed one clade and this clade is more closely related to L. starkeyi s.s. clade including one Japanese wild strain than other clades. Only three Japanese wild strains were genetically distinct from L. starkeyi. Lipomyces mesembrius and L. doorenjongii shared one clade, while L. kockii was genetically distinct from the other three species. Strains in L. starkeyi s.s. clade converted six sugars, d-glucose, d-xylose, l-arabinose, d-galactose, d-mannose, and d-cellobiose to produce high total lipid yields. The Japanese wild strains in subclades B, C, and D converted d-glucose, d-galactose, and d-mannose to produce high total lipid yields. Lipomyces mesembrius was divided into two subclades. Lipomyces mesembrius CBS 7737 converted d-xylose, l-arabinose, d-galactose, and d-cellobiose, while the other L. mesembrius strains did not. Lipomyces doorenjongii converted all the sugars except d-cellobiose. In comparison to L. starkeyi, L. mesembrius, and L. doorenjongii, L. kockii produced higher total lipid yields from d-glucose, d-galactose, and d-mannose. The type of sugar converted depended on the subclade classification elucidated in this study.

Evolutionary adaptation of recombinant shochu yeast for improved xylose utilization.

We examined the evolutionary adaptation of recombinant shochu yeast by serial anaerobic cultivation in xylose-based minimal medium. Compared with the parental strain, the adapted strain MA-S4-M1 (M1) markedly improved the growth on xylose and the anaerobic xylose consumption rate. M1 gained improved xylose utilization properties by optimizing the metabolic pathway enzymes and enhancing the uptake of xylose.

Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

A set of 15 new microsatellite loci was developed and characterized for the widespread mangrove tree species Sonneratia alba (Lythraceae) by using next-generation sequencing. Forty-eight S. alba samples from seven populations in the Indo-West Pacific region were genotyped; all loci were polymorphic, with the number of alleles ranging from three to eight. The mean observed heterozygosity per locus was 0.21 for a population from Sabah, Malaysia. No null allele or significant linkage disequilibrium was detected, indicating the robustness of the markers. Only one locus (SA103) showed deviation from Hardy–Weinberg equilibrium. As characterization of these microsatellite loci was done with samples covering most of the species’ distribution range, the markers can be applied to genetic diversity studies over the broad geographical range of the species.

Isolation and characterization of 14 microsatellite markers for Rhizophora mucronata (Rhizophoraceae) and their potential use in range-wide population studies

A set of 14 new microsatellite markers was developed for mangrove species Rhizophora mucronata (Rhizophoraceae) by using pyrosequencing. Fifty-six samples from 9 populations of R. mucronata in the Indo-West Pacific region were genotyped; all loci were polymorphic, with the number of alleles ranging from 2 to 9. The mean expected heterozygosity per locus was 0.16 in a population from Sabah, no significant linkage disequilibrium was found among loci, and significant deviation from Hardy–Weinberg equilibrium was found in 3 loci. The polymorphic microsatellite markers with samples covering most of the species’ distribution range can be applied in genetic diversity studies covering a broad geographical range of the species.

Phylogenetic and morphological reevaluation of Leucobryum boninense (Leucobryaceae), endemic to the Bonin Islands

Abstract Leucobryum boninense is an enigmatic species distributed in southeast China and islands of the northwestern Pacific and is the only species of Leucobryum known from the Bonin Islands which are typical oceanic islands. Molecular phylogenetic analysis using internal transcribed spacer (ITS) of nrDNA sequences was performed to resolve phylogenetic relationships among geographically isolated populations of L. boninense and its related species. The analysis showed that L. boninense is divided into two distinct clades, which correspond to geographical regions: an oceanic island clade (Bonin clade) and a continental region clade (Ryukyu clade). These two clades were also distinguished from each other by the ratio of the length of the prorate apex region to the whole leaf length, ecological preference and the colony habit. Plants of the Ryukyu clade proved to correspond to L. scaberulum, previously treated as a synonym of L. boninense. Molecular and morphological evidence strongly suggests that L. boninense is endemic to the Bonin Islands, and that L. scaberulum should be treated as a distinct species. Endemism of L. boninense on the oceanic islands may be result of allopatric speciation.

Geographical origin and sexual-system evolution of the androdioecious plant Gynochthodes boninensis (Rubiaceae), endemic to the Bonin Islands, Japan

Gynochthodes boninensis is a woody climber endemic to the Bonin Islands, Japan. It is characterized by an androdioecious sexual system, which is rare in angiosperms. We conducted a molecular phylogenetic analysis of 29 taxa including 61 samples from the tribe Morindeae to elucidate the geographical origin of G. boninensis by determining its progenitor species. We also investigated evolutionary transitions among different sexual systems within this plant group. The combined ETS, ITS, and trnT-F sequence data showed that G. boninensis formed a monophyletic group, but it did not form a clade with G. umbellata, which was treated as the same species, whereas it formed a clade with G. parvifolia, which is distributed in southeastern Asia. This suggests that G. boninensis evolved independently from G. umbellata, and probably originated from a progenitor native to southeastern Asia. In the clade composed of the three species of G. boninensis, G. parvifolia, and G. umbellata, only G. boninensis is androdioecious, whereas the others are dioecious. Thus, the androdioecious sexual system of G. boninensis may have evolved from dioecy.

Geographical origin of Leucobryum boninense Sull. & Lesq. (Leucobryaceae, Musci) endemic to the Bonin Islands, Japan.

Leucobryum boninense is endemic to the Bonin Islands, Japan, and its related species are widely distributed in Asia and the Pacific. We aimed to clarify the phylogenetic relationships among Leucobryum species and infer the origin of L. boninense. We also describe the utility of the chloroplast trnK intron including matK for resolving the phylogenetic relationships among Leucobryum species, as phylogenetic analyses using trnK intron and/or matK have not been performed well in bryophytes to date. Fifty samples containing 15 species of Leucobryum from Asia and the Pacific were examined for six chloroplast DNA regions including rbcL, rps4, partial 5′ trnK intron, matK, partial 3′ trnK intron, and trnL-F intergenic spacer plus one nuclear DNA region including ITS. A molecular phylogenetic tree showed that L. boninense made a clade with L. scabrum from Japan, Taiwan and, Hong Kong; L. javense which is widely distributed in East and Southeast Asia, and L. pachyphyllum and L. seemannii restricted to the Hawaii Islands, as well as with L. scaberulum from the Ryukyus, Japan, Taiwan, and southeastern China. Leucobryum boninense from various islands of the Bonin Islands made a monophylic group that was closely related to L. scabrum and L. javense from Japan. Therefore, L. boninense may have evolved from L. scabrum from Japan, Taiwan, or Hong Kong, or L. javense from Japan. We also described the utility of trnK intron including matK. A percentage of the parsimony-informative characters in trnK intron sequence data (5.8%) was significantly higher than that from other chloroplast regions, rbcL (2.4%) and rps4 (3.2%) sequence data. Nucleotide sequence data of the trnK intron including matK are more informative than other chloroplast DNA regions for identifying the phylogenetic relationships among Leucobryum species.

Development of 11 polymorphic microsatellite markers for Xylocarpus granatum (Meliaceae) using next-generation sequencing technology

Human impacts have seriously damaged mangroves, and conservation of mangroves will require information on local and regional population genetic structures. Here, we report the development and polymorphism of eleven novel microsatellite markers, developed using next-generation sequencing on 56 samples of widespread mangrove species Xylocarpus granatum (Meliaceae) from nine populations across the Indo-West Pacific region. All loci were found to be polymorphic, with the number of alleles per locus ranging from four to 19. In a population from Sabah (Malaysia), the mean observed and expected heterozygosity per locus was 0.59 and 0.58, respectively. No null allele, significant linkage disequilibrium or deviation from Hardy–Weinberg equilibrium was detected among all loci. The eleven markers developed can be valuable tools to conservation genetics of this species across its distributional range.

Description of the first Oriental species of the ant genus Xymmer (Hymenoptera: Formicidae: Amblyoponinae).

The monotypic ant genus Xymmer Santschi, 1914 was established for X. muticus (Santschi, 1914) which has so far been known only from the West African subregion. The genus is easily distinguishable from the other amblyoponine genera by the anteromedian part of clypeus which is produced as a short rectangular lobe. Additional undescribed species had been found exclusively from Madagascar and Africa until recently. However, in March, 2015, a Xymmer colony was found in northern Central Vietnam. In the present paper Xymmer phungi sp. nov. is described as the first Oriental species of the genus. Although the worker of X. phungi is morphologically quite similar to that of X. muticus, the former is distinguishable from the latter by the following two characteristics of the worker: clypeal lobe 1/6 times as long as broad (vs. 1/3 times as long as broad in X. muticus); anterior margin of the lobe weakly concave (vs. almost straight in X. muticus). Xymmer phungi is well distinguished from Ethiopian Xymmer spp. for which 28S sequences are available from GenBank. Our observations suggest that the species feeds on geophilids (Chilopoda: Geophilomorpha). An updated key to Vietnamese genera of the subfamily Amblyoponinae is also provided.

Microsatellite Markers for Leucobryum boninense (Leucobryaceae), Endemic to the Bonin Islands, Japan

Premise of the study: Microsatellite primers were developed for Leucobryum boninense, endemic to the Bonin Islands, Japan, to investigate its level of genetic diversity and population genetic structure. Methods and Results: Using next-generation sequencing, 21 primer sets were developed, among which nine loci were polymorphic in the populations of the Bonin Islands. Among these polymorphic loci, the number of alleles per locus ranged from two to 10 (mean = 3.444) and the expected heterozygosity ranged from 0.066 to 0.801 (mean = 0.338). Conclusions: These results indicate the utility of the nine microsatellite markers that we developed for population genetic studies of L. boninense.