The complete mitochondrial genome of a Biwa goby, Gymnogobius isaza (Tanaka, 1916).

We determined the complete mitochondrial DNA sequence of a Biwa goby, Gymnogobius isaza (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between G. isaza and G. petschiliensis. This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.

The draft genome sequence of the Brahminy blindsnake Indotyphlops braminus.

Blindsnakes of infraoder Scolecophidia (order Squamata) are the most basal group of extant snakes, comprising of more than 450 species with ecological and morphological features highly specialized to underground living. The Brahminy blindsnake, Indotyphlops braminus, is the only known obligate parthenogenetic species of snakes. Although the origin of I. braminus is thought to be South Asia, this snake has attracted worldwide attention as an alien species, as it has been introduced to all continents except Antarctica. In this study, we present the first draft genome assembly and annotation of I. braminus. We generated approximately 480 Gbp of sequencing data and produced a draft genome with a total length of 1.86 Gbp and N50 scaffold size of 1.25 Mbp containing 89.3% of orthologs conserved in Sauropsida. We also identified 0.98 Gbp (52.82%) of repetitive genome sequences and a total of 23,560 protein-coding genes. The first draft genome of I. braminus will facilitate further study of snake evolution as well as help to understand the emergence mechanism of parthenogenetic vertebrates.

The complete mitochondrial genome of a bagrid catfish, Tachysurus nudiceps, and its phylogenetic implications for the classification of the bagrid genera.

The complete sequence of the mitochondrial genome (mitogenome) of Tachysurus nudiceps (family Bagridae; order Siluriformes) was determined using next-generation sequencing. The composition of its mitogenome is the same as that observed in most other vertebrates and consists of 37 genes, an L-strand replication origin and a control region. As in previous studies, our phylogenetic analyses revealed that many of the bagrid genera are not monophyletic, emphasizing the necessity for reviewing and revising the taxonomy of this family at the genus level.

Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.

Exceptional Enlargement of the Mitochondrial Genome Results from Distinct Causes in Different Rain Frogs (Anura: Brevicipitidae: Breviceps).

The mitochondrial (mt) genome of the bushveld rain frog (Breviceps adspersus, Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions. To investigate the evolutionary lineage, timing, and process of mt genome enlargement, we sequenced the complete mtDNAs of two congeneric rain frogs, B. mossambicus and B. poweri. The mt genomic organization, gene content, and gene arrangements of these two rain frogs are very similar to each other but differ from those of B. adspersus. The B. mossambicus mt genome (22.5 kbp) does not differ significantly from that of most other afrobatrachians. In contrast, the B. poweri mtDNA (28.1 kbp) is considerably larger: currently the second largest among vertebrates, after B. adspersus. The main causes of genome enlargement differ among Breviceps species. Unusual elongation (12.5 kbp) of the control region (CR), a single major noncoding region of the vertebrate mt genome, is responsible for the extremely large mt genome in B. poweri. Based on the current Breviceps phylogeny and estimated divergence age, it can be concluded that the genome enlargements occurred independently in each species lineage within relatively short periods. Furthermore, a high nucleotide substitution rate and relaxation of selective pressures, which are considered to be involved in changes in genome size, were also detected in afrobatrachian lineages. Our results suggest that these factors were not direct causes but may have indirectly affected mt genome enlargements in Breviceps.

Evaluating the ontogenetic external morphology of an ectoparasitic Torix tukubana (Hirudinida: Glossiphoniidae), with records of its new host amphibian species.

Torix is a leech genus containing freshwater proboscidate species, and several members of this taxon are ectoparasites specific to amphibians. Torix tukubana inhabits mountain streams in Japan, and only two frog species are known to be hosts. We collected this leech from two other amphibians, Onychodactylus japonicus (Japanese clawed salamander) and Rana ornativentris (montane brown frog), for the first time. This finding suggests that the host specificity of T. tukubana is low. The immature individuals of T. tukubana were also collected and identified based on DNA data. This is the first juvenile record of this species confirmed by its DNA barcode sequences. Several morphological characters known from large individuals and used as diagnostic characteristics in taxonomic keys were not observed in the juveniles, suggesting that these are ontogenetic traits.