Isolation of purple non-sulfur bacteria from the digestive tract of ayu (Plecoglossus altivelis)

Purple non-sulfur bacteria (PNSB) reportedly have probiotic effects in fish, but whether they are indigenous in the digestive tract of fish is a question that requires answering. We attempted to isolate PNSB from the digestive tract of ayu (Plecoglossus altivelis) from the Kuma River (Kumamoto, Japan), and successfully isolated 12 PNSB strains. All the isolated PNSB belonged to the genus Rhodopseudomonas. Five Rhodopseudomonas strains were also isolated from the soil samples collected along the Kuma River. The phylogenetic tree based on the partial sequence of pufLM gene indicated that the PNSB from ayu and soil were similar. The effects of NaCl concentration in growth medium on growth were also compared between the PNSB from ayu and soil. The PNSB from ayu showed a better growth performance at a higher NaCl concentration, suggesting that the intestinal tract of ayu, a euryhaline fish, might provide suitable environment for halophilic microorganisms.

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

The effects of long-term translocation on population genetic structure of Ayu in Japan: Management implications for a recreationally fished iconic species

Ayu (Plecoglossus altivelis altivelis), an important freshwater fisheries resource and popular recreational fishing species, lives for only one year and has a single breeding season. To supplement increased recreational fishing demand, huge numbers of wild–born landlocked juvenile Ayu have been translocated from Lake Biwa into most Japanese rivers for more than 50 generations. Hatchery-born amphidromous fish (including amphidromous and landlocked form hybrids) have also been released for many generations. Hatchery–born fish have low survival and maladapted behaviour in the wild. Landlocked and amphidromous forms of Ayu easily hybridise, but survival of progeny of landlocked forms is very low in seawater. Repeat backcrossing may cause introgression of landlocked forms into amphidromous populations, but this has not been previously identified. Study objectives using genetic data from Ayu from 118 locations throughout the distribution of this species in Japan are to describe contemporary population structure, genetic diversity, and admixture proportions of Ayu forms in populations, and to evaluate how human-induced translocation has affected population genetic structure. The analyses of published genotypes of 12 microsatellite markers provide strong evidence for very high gene flow between populations, but population structure has been retained in several regions, and several populations are nested. Genetic diversity is surprisingly homogeneous. Hybridisation between landlocked and amphidromous forms has occurred in all populations, with a mean hybrid proportion (± standard deviation) of 37 ± 10%, ranging 15%–60%. Results are discussed in relation to the conservation and management of this species. Recommendations are made to reduce translocation and hatchery releases, by establishing rivers and/or areas in every prefecture where translocation does not occur. Release of juveniles is of value for short–term management objectives, but management of spawning escapements, and improving the spawning and nursery habitat are important for this species long–term sustainability.