BackgroundIn Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs.ResultsWe generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens.ConclusionsThis is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.

BackgroundThe plastid acquisition by secondary endosymbiosis is a driving force for the algal evolution, and the comparative genomics was required to examine the genomic change of symbiont. Therefore, we established a pipeline of a de novo assembly of middle-sized genomes at a low cost and with high quality using long and short reads.ResultsWe sequenced symbiotic algae Chlorella variabilis using Oxfofrd Nanopore MinION as the long-read sequencer and Illumina HiSeq 4000 as the short-read sequencer and then assembled the genomes under various conditions. Subsequently, we evaluated these assemblies by the gene model quality and RNA-seq mapping rate. We found that long-read only assembly could not be suitable for the comparative genomics studies, but with short reads, we could obtain the acceptable assembly. On the basis of this result, we established the pipeline of de novo assembly for middle-sized algal genome using MinION.ConclusionsThe genomic change during the early stages of plastid acquisition can now be revealed by sequencing and comparing many algal genomes. Moreover, this pipeline offers a solution for the assembly of various middle-sized eukaryotic genomes with high-quality and ease.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5067-1) contains supplementary material, which is available to authorized users.

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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.

Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.

Growth hormone (GH) transgenesis can be used to manipulate the growth performance of fish and mammals. In this study, homozygous and hemizygous GH-transgenic amago salmon (Oncorhynchus masou ishikawae) derived from a single female exhibited hypoglycemia. Proteomic and signal network analyses using iTRAQ indicated a decreased NAD+/NADH ratio in transgenic fish, indicative of reduced mitochondrial ND1 function and ROS levels. Mitochondrial DNA sequencing revealed that approximately 28% of the deletion mutations in the GH homozygous- and hemizygous-female-derived mitochondrial DNA occurred in ND1. These fish also displayed decreased ROS levels. Our results indicate that GH transgenesis in amago salmon may induce specific deletion mutations that are maternally inherited over generations and alter energy production.

Otter clam farming in Vietnam has recently encountered difficulties due to swollen-siphon disease. Here, we report the metagenome sequences of microorganisms extracted from the siphon tissue of infected otter clams. The data comprised bacterial and viral sequences which likely include those derived from the disease-causing agent.

Background: Photosynthetic eukaryotes have evolved through the acquisition of plastids by secondary endosymbiosis, a process that requires several steps. Immediately before plastid acquisition, the genome of the symbiont is known to be dramatically reduced, but few studies have focused on the genomic changes in the symbiont at the early stages of secondary endosymbiosis. Methods: To investigate the genetic basis of the transition from facultative to obligate endosymbiosis, we compared the genomes of Chlorella variabilis, a representative symbiotic alga, with that of Paramecium bursaria, to compare closely related free-living species and transcriptomes between organisms in symbiotic and non-symbiotic conditions. Results: We found that the non-reduced genome of C. variabilis and its genes play a crucial role in endosymbiosis, being involved in cell wall biogenesis and degradation, and metabolic exchanges with the host. Our results suggest that the genetic mechanism underlying the enhancement of photosynthesis under symbiosis is the increasing light absorption efficiency and carbon fixation capacity of the endosymbiont, resulting in an increase in the supply of maltose to P. bursaria.