Flushing emissions of methane and carbon dioxide from mangrove soils during tidal cycles.

Mangroves are transition areas connecting land, freshwater, and the ocean, where a great amount of organic carbon accumulates in the soil, forming a considerable carbon sink. However, the soil might also be a source of greenhouse gas (GHG) emissions. This study hypothesized that measuring GHG emissions solely during low tides can represent diurnal GHG emissions in mangroves. Methane (CH4) and carbon dioxide (CO2) emissions were quantified during tidal cycles using an ultraportable gas analyzer in Kandelia obovata (without pneumatophores) and Avicennia marina (with pneumatophores) mangroves in summer and fall. The results showed that the CH4 fluxes varied greatly during tidal cycles, from -1.25 to 96.24 µmol CH4 m-2 h-1 for K. obovata and from 2.86 to 2662.00 µmol CH4 m-2 h-1 for A. marina. The CO2 fluxes ranged from -4.23 to 20.65 mmol CO2 m-2 h-1 for K. obovata and from 0.09 to 24.69 mmol CO2 m-2 h-1 for A. marina. The diurnal variation in GHG levels in mangroves is predominantly driven by tidal cycles. The peak emissions of CH4 and CO2 were noted at the beginning of the flooding tide, rather than during daytime or nighttime. While the patterns of the CO2 fluxes during tidal cycles were similar between K. obovata and A. marina mangroves, their CH4 flux patterns during the tidal cycles differed. Possibly due to different transport mechanisms, CO2 emissions are primarily influenced by surface soils, whereas CH4 is predominantly emitted from deeper soils, thus being influenced by root structures. To reduce the uncertainty in measuring GHG emissions in mangrove soils during a tidal cycle, it is advisable to increase the number of GHG flux measurements during the period spanning 30 min before and after the beginning of the flooding and ebbing tides.

Regulation of PGC-1α of the Mitochondrial Energy Metabolism Pathway in the Gills of Indian Medaka (Oryzias dancena) under Hypothermal Stress.

Ectothermic fish exposure to hypothermal stress requires adjusting their metabolic molecular machinery, which was investigated using Indian medaka (Oryzias dancena; 10 weeks old, 2.5 ± 0.5 cm) cultured in fresh water (FW) and seawater (SW; 35‱) at room temperature (28 ± 1 °C). The fish were fed twice a day, once in the morning and once in the evening, and the photoperiod was 12 h:12 h light: dark. In this study, we applied two hypothermal treatments to reveal the mechanisms of energy metabolism via pgc-1α regulation in the gills of Indian medaka; cold-stress (18 °C) and cold-tolerance (extreme cold; 15 °C). The branchial ATP content was significantly higher in the cold-stress group, but not in the cold-tolerance group. In FW- and SW-acclimated medaka, the expression of genes related to mitochondrial energy metabolism, including pgc-1α, prc, Nrf2, tfam, and nd5, was analyzed to illustrate differential responses of mitochondrial energy metabolism to cold-stress and cold-tolerance environments. When exposed to cold-stress, the relative mRNA expression of pgc-1α, prc, and Nrf2 increased from 2 h, whereas that of tfam and nd5 increased significantly from 168 h. When exposed to a cold-tolerant environment, prc was significantly upregulated at 2 h post-cooling in the FW and SW groups, and pgc-1α was significantly upregulated at 2 and 12 h post-cooling in the FW group, while tfam and nd5 were downregulated in both FW and SW fish. Hierarchical clustering revealed gene interactions in the cold-stress group, which promoted diverse mitochondrial energy adaptations, causing an increase in ATP production. However, the cold-tolerant group demonstrated limitations in enhancing ATP levels through mitochondrial regulation via the PGC-1α energy metabolism pathway. These findings suggest that ectothermic fish may develop varying degrees of thermal tolerance over time in response to climate change. This study provides insights into the complex ways in which fish adjust their metabolism when exposed to cold stress, contributing to our knowledge of how they adapt.

Complete mitochondrial genome of Rasbora trilineata (Cypriniformes, Cyprinidae).

We describe the complete mitochondrial genome sequence of Rasbora trilineata, which is a small cyprinid popular in aquarium trade. The circle genome (16,747 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The overall base composition of R. trilineata is 25.35% for T, 26.43% for C, 33.57% for A, and 14.65% for G, with a slight AT bias of 58.92%.

Complete mitochondrial genome of Oncorhynchus masou formosanus (Jordan & Oshima, 1919) (Pisces, Salmonidae).

We describe the complete mitochondrial genome sequence of Oncorhynchus masou formosanus, which is a critically endangered landlocked salmon of Taiwan by using next-generation sequencing. The circle genome (16,653 bp) has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding control region. The overall base composition of O. m. formosanus is 28.6% for A, 26.8% for T, 16.5% for G and 28.1% for C, with a slight AT bias of 55.4%.

Complete mitochondrial DNA genome of Onychostoma sima (Cypriniformes: Cyprinidae).

In this study, we sequenced the complete mitochondrial genome of Onychostoma sima (Cypriniformes, Cyprinidae). This mitochondrial genome, consisting of 16,601 base pairs (bp), encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a noncoding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 934 bp lengths long, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows 24.30% of T, 28.28% of C, 31.31% of A and 16.11% of G, with a slight AT bias of 55.61%.

Complete mitochondrial DNA genome of Microphysogobio brevirostris (Cypriniformes: Cyprinidae).

In this study, we sequenced the complete mitochondrial genome of Microphysogobio brevirostris (Cypriniformes, Cyprinidae), an endemic primary freshwater fish in Taiwan. This mitochondrial genome, consisting of 16,608 base pairs (bp), encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 929 bp lengths long, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 26.28%, C 26.62%, A 30.26%, and G 16.85%, with a slight AT bias of 56.53%.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.

Development of 12 genic microsatellite loci for a biofuel grass, Miscanthus sinensis (Poaceae).

PREMISE OF THE STUDY: Miscanthus, a nonfood plant with high potential as a biofuel, has been used in Europe and the United States. The selection of a cultivar with high biomass, photosynthetic efficiency, and stress resistance from wild populations has become an important issue. New genic microsatellite markers will aid the assessment of genetic diversity for different strains. METHODS AND RESULTS: Twelve polymorphic microsatellite markers derived from the transcriptome of Miscanthus sinensis fo. glaber were identified and screened on 80 individuals of M. sinensis. The number of alleles per locus ranged from 6 to 12, and the mean expected heterozygosity was 0.75. Cross-taxa transferability revealed that all loci can be applied to all varieties of M. sinensis, as well as the closely related species M. floridulus. CONCLUSIONS: These new genic microsatellite markers are useful for characterizing different traits in breeding programs or to select genes useful for biofuel.

Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.

• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.