Biology subjects

Terai, Y.

Publications and source records attributed to Terai, Y..

6 recordsLinked to original sources

bioRxiv2023

Genome analysis of the Jomon dogs reveals the oldest domestic dog lineage in Eastern Eurasia

Dog is the oldest domesticated animal that established close relationships with humans. Due to its ancient origin, when, where, and whether a single or dual domestication event occurred is still under debate. The dogs in the Jomon period (Jomon dogs) in the Japanese archipelago had little change in morphology from 10,000 to 3,000 years ago. Therefore, we expected that the ancient genome of the Jomon dogs would provide a clue to reveal the characteristics of the ancient East Asian dogs. Here, we have sequenced the genomes of three 6000-year-old Jomon dogs, one 3000-4000-year-old Jomon dog, and four late 8th century dogs excavated in Japan. Our analyses suggest that the Jomon dogs are a distinct lineage from the previously known ancient dogs and are one of the oldest among the dogs in East Eurasian lineages. In addition, the genome of the Jomon dogs contained 9.5% of the genome of Japanese wolf ancestry due to a single introgression event. We estimated the proportion of the Jomon dog lineage genome in the genomes of dogs, which indicates that the genomic composition derived from the Jomon dog lineage is one of the major sources of modern dog genomes. Furthermore, we estimated the early admixture events of dogs in East Eurasia by analyzing the ancient genomes of the Jomon dogs. Due to the admixture events, the Jomon dog-derived genome has been one of the genomic sources of a wide range of modern dogs.

evolutionary biology↗

bioRxiv2023

Visual adaptation of opsin gene expression to the aquatic environment in sea turtles

Several vertebrate taxa, cetaceans, sirenia, pinnipeds, and sea snakes have adapted to the marine aquatic environment. In the species of these taxa, marine adaptation has resulted in shifts in the absorption spectra of opsin pigments and/or the degeneration or duplication of opsin genes. Thus, marine adaptation has strongly affected the evolution of opsins. In sea turtles, however, the effect of adaptation from freshwater to marine environments on opsin evolution has not been studied. In this study, we determined the high-throughput RNA sequences extracted from eyes of two sea turtles (green turtle: Chelonia mydas, loggerhead: Caretta caretta) and two freshwater turtle species (three-keeled pond turtle: Mauremys reevesii, softshell turtle: Pelodiscus sinensis) and investigated the amino acid evolution and expression of the opsin gene. We found that most of the sea turtle lineage-specific amino acid substitutions did not alter amino acid properties and did not include previously known substitutions for turning absorption spectra of opsin pigments, suggesting no adaptive amino acid substitutions in the opsins during marine adaptation in sea turtles. Instead, the blue-sensitive opsin (SWS2) gene expression was higher in sea turtles than in freshwater turtles. These results suggest that sea turtles may have adapted their vision to the blue light-rich marine environment by increasing SWS2 expression.

evolutionary biology↗

bioRxiv2023

Comparative genomics of two closely related coral species with different spawning seasons reveals genomic regions possibly associated with gametogenesis

Marine invertebrates release their gametes at an optimal time to produce the next generation. In reef-building scleractinian corals, synchronous spawning is essential for reproductive success. Molecular mechanisms of scleractinian gametogenesis have been studied; however, the mechanism by which coral gametes mature at specific times has yet to be discovered. The present study focused on two Acropora species with different spawning seasons. In Okinawa, Japan, Acropora digitifera spawns from May to June, whereas Acropora sp. 1 spawns in August. Comparative genomic analyses revealed that 39 candidate genes are differentiated between the two species, suggesting a possible association with timing of gametogenesis. Among candidate genes, we identified an Acropora sp. 1-specific amino acid change in gene WDR59, one of the components of a mTORC1 activator, GATOR2. Since regulation of gametogenesis by mTORC1 is widely conserved among eukaryotes, the difference in timing of gamete maturation observed in the two Acropora species may be caused by a substitution in WDR59 that slightly affects timing of mTORC1 activation via GATOR2. In addition, this substitution may lead to reproductive isolation between the two species, due to different spawning periods. Thus, we propose that A. digitifera and Acropora sp. 1 species pair is an effective model for studying coral speciation and understanding the molecular mechanisms that control coral spawning timing. Significance statement (required)For successful coral reproduction, conspecific corals must spawn synchronously. Gamete production initiates coral spawning. Regulation of gamete maturation by a protein complex, mTORC1, is widely conserved among organisms, but little is known about it in cnidarians. In this study, we analyzed genomes of two closely related Acropora species with different spawning months, May/June and August. Our analyses revealed that 39 genes are genetically differentiated between the two species. One of these is a component of mTORC1 activator, suggesting that this gene may be associated with the difference in spawning times of these two species.

evolutionary biology↗

bioRxiv2023

The third symbiotic partner of the volcano lichen Cladonia vulcani Savicz drove adaptation to an extreme environment.

Chemosynthetic symbioses between sulfur-oxidizing bacteria and aquatic eukaryotes have been discovered globally in sulfide-rich environments, notably deep-sea hydrothermal vents, cold seeps, and sulfidic cave systems. However, to the best of our knowledge, such chemosymbiotic lifestyles have not been reported from terrestrial eukaryotes. Here we report that the volcano lichen Cladonia vulcani Savicz ubiquitously associates with a single bacterial species that could potentially use hydrogen sulfide as a source of energy. We identified sequences of the bacterium in all 27 samples collected from five geothermal areas across Japan with cellular abundance comparable to the fungal partner. The assembled bacterial genome contained genes involved in sulfur oxidation. The stable association with a potential sulfur-oxidizer is likely to represent an obligate tripartite symbiotic system consisting of fungal, algal, and bacterial partners that has enabled adaptation to the extreme environment.

evolutionary biology↗

bioRxiv2022

Adaptation of the eyes of grass puffer (Takifugu niphobles) to the riverine and marine environments

Many marine fish species migrate to rivers, but little is known about whether these species switch their vision when inhabiting rivers or adapt their vision to the environment of both rivers and the sea. Grass puffer (Takifugu niphobles) is a marine fish species frequently migrating to rivers. In this study, we investigated grass puffers from riverine and marine populations and analyzed the gene expression in their eyes. The phylogeny and population genetics of riverine and marine grass puffers indicated that riverine and marine grass puffers are from the same population. Gene expression levels by high-throughput RNA sequencing indicated no differences in the expression patterns of vision-related genes in marine and riverine grass puffers. This result indicates that the adaption of their visual system to both marine and riverine environments rather than switching the expression of vision-related genes. Additionally, riverine grass puffers increase the expression levels of heat shock proteins and related genes. These genes showed higher expression in riverine grass puffer than in other marine and river pufferfish species, suggesting that the grass puffer individuals adapt to the environmental difference when they migrate to the river by increasing the expression levels of heat shock protein and related genes.

evolutionary biology↗

bioRxiv2021

The Japanese wolf is most closely related to modern dogs and its ancestral genome has been widely inherited by dogs throughout East Eurasia

The Japanese wolf (Canis lupus hodophilax Temminck, 1839) was a subspecies of the gray wolf that inhabited the Japanese Archipelago and became extinct 100-120 years ago. In this study, we determined the whole genomes of nine Japanese wolves from the 19th- early 20th centuries and 11 Japanese dogs and analyzed them along with both modern and ancient wolves and dogs. Genomic analyses indicate that the Japanese wolf was a unique subspecies of the gray wolf that was genetically distinct from both modern and ancient gray wolves, lacking gene flow with other gray wolves. A Phylogenetic tree that minimizes the effects of introgression shows that Japanese wolves are closest to the dog monophyletic group among the gray wolves. Moreover, Japanese wolves show significant genetic affinities with East Eurasian dogs. We estimated the level of introgression from the ancestor of the Japanese wolves to the ancestor of East Eurasian dogs that had occurred in the transitional period from the Pleistocene to the Holocene, at an early stage after divergence from West Eurasian dog lineages. Because of this introgression, Japanese wolf ancestry has been inherited by many dogs through admixture between East Eurasian dog lineages. As a result of this heredity, up to 5.5% of modern dog genomes throughout East Eurasia are derived from Japanese wolf ancestry.

evolutionary biology↗