Chromosome-level genome assembly of Patagonian moray cod (Muraenolepis orangiensis) and immune deficiency of major histocompatibility complex (MHC) class II

The Patagonian moray cod, Muraenolepis orangiensis, belongs to the family Muraenolepididae and is the sole order of Gadiformes that inhabits the temperate and cold waters of the southern hemisphere. One of the features of the Gadiformes order is that they have a remarkably unique immune gene repertoire that influences innate and adaptive immunity, and they lack major histocompatibility complex (MHC) class II, invariant chains (CD74), and CD4 genes. In this study, a high-quality chromosome-level genome assembly was constructed, resulting in a final assembled genome of 893.75 Mb, with an N50 scaffold length of 30.07 Mb and the longest scaffold being 39.77 Mb. Twenty-five high-quality pseudochromosomes were assembled, and the complete BUSCO rate was 93.4%. A total of 34,553 genes were structurally annotated, and 27,691 genes were functionally annotated. Among the 10 primary genes involved in MHC class II, only two ERAP1 genes and one AIRE gene were identified through the genome study. Although no specific reason for the MHC class II deficiency has been identified, it has been shown that the toll-like receptors (TLRs), which are significant to the innate immune response, are significantly expanded in M. orangiensis. A total of 44 TLRs have been identified, with 32 TLR13 genes distributed evenly on six different pseudochromosomes. This study is the first to reveal the whole genome of a Muraenolepididae family and provides valuable insights into the potential rationale for the MHC class II deficiency in a Gadiformes fish species

Sex-Biased Gene Expression and Isoform Profile of Brine Shrimp Artemia franciscana by Transcriptome Analysis

The brine shrimp Artemia has a ZW sex determination system with ZW chromosomes in females and ZZ chromosomes in males. Artemia has been considered a promising model organism for ZW sex-determining systems, but the genes involved in sex determination and differentiation of Artemia have not yet been identified. Here, we conducted transcriptome sequencing of female and male A. franciscana using PacBio Iso-Seq and Illumina RNA-Seq techniques to identify candidate sex determination genes. Among the 42,566 transcripts obtained from Iso-Seq, 23,514 were analyzed. Of these, 2065 (8.8%) were female specific, 2513 (10.7%) were male specific, and 18,936 (80.5%) were co-expressed in females and males. Based on GO enrichment analysis and expression values, we found 10 female-biased and 29 male-biased expressed genes, including DMRT1 and Sad genes showing male-biased expression. Our results showed that DMRT1 has three isoforms with five exons, while Sad has seven isoforms with 2–11 exons. The Sad gene is involved in ecdysteroid signaling related to molting and metamorphosis in arthropods. Further studies on ecdysteroid biosynthetic genes are needed to improve our understanding of Artemia sex determination. This study will provide a valuable resource for sex determination and differentiation studies on Artemia and other crustaceans with ZW systems

The complete mitochondrial genome of Cacopsylla burckhardti (Hemiptera, Psylloidea, Psyllidae)

Cacopsylla burckhardti Luo, Li, Ma & Cai, 2012 (Hemiptera, Psylloidea, Psyllidae) is a pear psyllid species, distributed in the East Asia. The complete mitogenome of C. burckhardti is obtained in this study for the first time. The mitogenome of C. burckhardti is circular form and 14,798 bp long, which consists of 13 protein-coding genes, 22 tRNAs and two rRNAs. The base composition is 38.80% for A, 34.89% for T, 9.99% for G and 16.33% for C, with the higher A + T contents (73.69%). The phylogenetic analysis, using 13 protein-coding genes, shows that C. burckhardti is clustered with other Cacopsylla species and nested in the Psyllidae clade within the superfamily Psylloidea

The complete mitochondrial genome of Cacopsylla burckhardti (Hemiptera, Psylloidea, Psyllidae)

Cacopsylla burckhardti Luo, Li, Ma & Cai, 2012 (Hemiptera, Psylloidea, Psyllidae) is a pear psyllid species, distributed in the East Asia. The complete mitogenome of C. burckhardti is obtained in this study for the first time. The mitogenome of C. burckhardti is circular form and 14,798 bp long, which consists of 13 protein-coding genes, 22 tRNAs and two rRNAs. The base composition is 38.80% for A, 34.89% for T, 9.99% for G and 16.33% for C, with the higher A + T contents (73.69%). The phylogenetic analysis, using 13 protein-coding genes, shows that C. burckhardti is clustered with other Cacopsylla species and nested in the Psyllidae clade within the superfamily Psylloidea

The complete mitochondrial genome of the Arctic fairy shrimp Branchinecta paludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinecta paludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B. paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B. paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B. paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans

The complete mitochondrial genome of the Antarctic fairy shrimp Branchinecta gaini Daday, 1910 (Branchiopoda, Anostraca, Branchinectidae)

The complete mitochondrial genome of Antarctic fairy shrimp Branchinecta gaini Daday, 1910 was sequenced, assembled and annotated using next-generation sequencing technology. The mitogenome of B. gaini is circular at 15,536 bp in length, consisting of 13 protein-coding genes, 23 tRNAs, two rRNAs and two major non-coding regions. In particular, there are two tRNAGly genes and one non-coding region between these two tRNAGly genes. A phylogenetic tree was constructed using concatenated amino acid sequences of 13 protein-coding genes. It reveals that B. gaini is clustered with the Anostraca group within the Branchiopoda clade. This study helps us understand the evolution of Anostraca

Effectiveness and safety of exenatide in Korean patients with type 2 diabetes inadequately controlled with oral hypoglycemic agents: an observational study in a real clinical practice

Abstract Background Randomized clinical trials have shown the efficacy and safety of short-acting exenatide in patients with type 2 diabetes mellitus (T2DM). The aim of this observational study was to investigate the effectiveness and safety of exenatide twice a day in Korean patients with T2DM who are suboptimally controlled with oral hypoglycemic agents. Methods This study was a post hoc analysis of multi-center (71 centers), prospective, observational, single-arm, post-marketing study of short-acting exenatide 5 to 10 μg twice a day from March 2008 to March 2014 and analyzed those who finished the follow-up over 20 weeks of medication. Changes of hemoglobin A1c (HbA1c), fasting plasma glucose (FPG), and body weight values before and after exenatide treatment were analyzed. Adverse events and adverse drug reactions were estimated in patients who were treated with exenatide at least once and for whom follow-up for safety has been completed. Results After 20 weeks treatment with exenatide, mean HbA1c and body weight were significantly reduced from 8.4% to 7.7% and from 83.4 kg to 80.2 kg, respectively (both p < 0.001). Subjects with higher baseline glucose and HbA1c levels showed an independent association with a greater reduction in glucose level. In addition, short duration of diabetes less than 5 years was an independent predictor for the improvement in glucose level. The majority of study subjects showed a reduction in both body weight and glucose level (63.3%) after exenatide treatment. In terms of safety profile, exenatide treatment was generally well-tolerated and the incidence of severe adverse event was rare (0.8%). The gastrointestinal side effects were most common and hypoglycemia was reported in 1.7% of subjects. Conclusion In real clinical practice, 20 weeks treatment with short-acting exenatide was well tolerated and showed a significant body weight and glucose reduction in Korean patients with T2D who are suboptimally controlled with oral hypoglycemic agents. Trial registration ClinicalTirals.gov , number NCT02090673 , registered 14 February 2008

Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis)

The Muraenolepididae family of fishes, known as eel cods, inhabits continental slopes and shelves in the Southern Hemisphere. This family belongs to the Gadiformes order, which constitutes one of the most important commercial fish resources worldwide, but the classification of the fish species in this order is ambiguous because it is only based on the morphological and habitat characteristics of the fishes. Here, the genome of Patagonian moray cod was sequenced using the Illumina HiSeq platform, and screened for microsatellite motifs. The genome was predicted to be 748.97 Mb, with a heterozygosity rate of 0.768%, via K-mer analysis (K = 25). The genome assembly showed that the total size of scaffolds was 711.92 Mb and the N50 scaffold length was 1522 bp. Additionally, 4,447,517 microsatellite motifs were identified from the genome survey assembly, and the most abundant motif type was found to be AC/GT. In summary, these data may facilitate the identification of molecular markers in Patagonian moray cod, which would be a good basis for further whole-genome sequencing with long read sequencing technology and chromosome conformation capture technology, as well as population genetics

A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus

Abstract The blackfin Icefish (Chaenocephalus aceratus) belongs to the family Channichthyidae and the suborder Notothenioidei which lives in the Antarctic. We corrected the mis-scaffolds in the previous linkage map results by Hi-C analysis to obtain improved results for chromosome-level genome assembly. The final assembly analysis resulted in a total of 3,135 scaffolds, a genome size of 1,065.72 Mb, and an N50 of 33.46 Mb. 820.24 Mb, representing 88.88% of the total genome, is anchored to 24 chromosomes. The final gene set of 38,024 genes, including AFGPs, was annotated using RNA evidence, proteins, and ab-initio predictions. The complete percentage of BUSCO analysis is 92.7%. In this study, we aim to contribute to the study of polar fishes by improving the genome sequences of the blackfin icefish with the AFGP genes belonging to the Notothenoidei

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, <i>Chionobathyscus dewitti</i>

The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers