The re-description of Synoecnema hirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships

Synoecnema hirsutum Timm, 1959 (Ungellidae, Drilonematoidea), found in the body cavity of the pheretimoid earthworm at the border of Laos and Vietnam, was re-described and illustrated. The mitochondrial genome of S. hirsutum obtained with Illumina HiSeq sequencing is the first annotated mitochondrial genome as a representative of the superfamily Drilonematoidea. The phylogeny inferred from the analysis of 12 mitochondrial genes has shown some similarity of S. hirsutum with a cephalobid Acrobeloides varius.

Bacterial communities in the polluted area of pyrite tailings: From the upstream, pollutant source, and to the downstream

Pyrite tailings can cause serious pollution to the surface water as the strong acidity, high iron and sulfate concentration in the leachate. The bacterial communities of pyrite tailings polluted area were still unclear which could restrict the recognition of the pyrite tailings pollution effect and further impede the development of microbial or ecology treatment technologies. In this study, the bacterial communities in the polluted area of pyrite tailings, from the upstream, pollutant source, and to the downstream, were analyzed with Illumina HiSeq sequencing. Results showed that Acinetobacter and Flavobacterium were abundant in the water and sediment of upstream and downstream while Bacteroides, Lactobacillus, and Akkermansia were abundant in the pollutant source. Sulfur-metabolizing or iron-metabolizing bacteria extensively existed in the polluted area in which Acidiferrobacter, Ferrithrix, and Desulfovibrio played crucial roles on the whole communities. Sulfur-metabolizing bacteria (e.g. Thiomonas, Sulfurospirillum, and Desulfobulbus) and iron-metabolizing bacteria (e.g. Ferrimicrobium, Ferrithrix, and Ferrovum) were introduced to the river polluted by pyrite tailings. Pyrite tailings can remarkably change the physicochemical characteristics and bacterial communities of river water and sediment.

Complete genome of Xanthomonas arboricola pv. corylina strain A7 isolated from southern Chile

The complete genome sequence of Xanthomonas arboricola pv. corylina A7 was obtained by a hybrid approach combining Pacbio and Illumina HiSeq sequencing data. A single circular chromosome of 5.1 mb with 65.47% G+C content was obtained. We identified 4344 coding sequences and some genes involved in copper resistance. To our knowledge, the data presented herein is the first report of high-quality whole genome of X. arboricola pv. corylina, isolated from infected hazelnut trees in southern Chile.

Comparative Transcriptomic and Expression Profiles Between the Foot Muscle and Mantle Tissues in the Giant Triton Snail Charonia tritonis

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Limited research on molecular mechanisms can be conducted because the complete genomic information on this species is unavailable. Hence, we performed transcriptome sequencing of the C. tritonis foot muscle and mantle using the Illumina HiSeq sequencing platform. In 109,722 unigenes, we detected 7,994 (3,196 up-regulated and 4,798 down-regulated) differentially expressed genes (DEGs) from the C. tritonis foot muscle and mantle transcriptomes. These DEGs will provide valuable resources to improve the understanding of molecular mechanisms involved in biomineralization of C. tritonis. In the Gene Ontology (GO) database, DEGs were clustered into three main categories (biological processes, molecular functions, and cellular components) and were involved in 50 functional subcategories. The top 20 GO terms in the molecular function category included sulfotransferase activity, transferring sulfur-containing groups, and calcium ion binding, which are terms considered to be related to biomineralization. In KEGG classifications, transcriptomic DEGs were mainly enriched in glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate, and sulfur metabolism pathway, which may be related to biomineralization. The results of qPCR showed that three of the eight genes examined were significantly up-regulated in the mantle. The phylogenetic tree of BMP1 suggested a significant divergence between homologous genes in C. tritonis. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms such as reproduction.

Integument transcriptome profile of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata)

In non-model organisms, Next Generation Sequencing (NGS) technology improve our ability to analyze gene expression and identify new genes or transcripts of interest. In this research, paired-end Illumina HiSeq sequencing has been used to describe a composite transcriptome based on two libraries generated from dorsal and ventral integuments of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata). A total of 43,044,977 million HQ reads were initially generated. After de novo assembly, a total of 111,194 unigenes were predicted. On all predicted unigenes, 32,569 show significant matches with genes/proteins present in the reference databases. Around 50% of annotated unigenes were significantly similar to sequences from the purple sea urchin Strongylocentrotus purpuratus genome. Annotation analyses were performed on predicted unigenes using public reference databases. These RNA-seq data provide an interesting resource for researchers with a broad interest in sea cucumber biology.

Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in disease such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin primary microRNAs are challenging to study in clinical samples where input material is limited.Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA using as little as 500 thousand Illumina HiSeq sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma.We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease. With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.

Comparison of the Gut Microbiota Composition Between Captive and Wild Roe Deer

ABSTRACTIn this paper, 16S-rRNA gene Illumina HiSeq sequencing was used to analyze the structural diversity of captive and wild roe deer gut flora. The results show that the microbial diversity in the feces of wild roe deer is higher than in that of captive roe deer. Both roe deer have similar flora at the phylum level, but the main genus has significant differences. The microbial group that plays an important role in captive roe deer is Bacteroidetes; in wild roe deer it is Firmicutes. This difference is mainly due to the differences in living environment, diet, and physiological functions of the two groups. In conclusion, our study makes people have a better understanding of the intestinal flora of roe deer. By comparing the intestinal microbial structure differences between captive and wild roe deer, it provides theoretical basis for people to raise captive roe deer and provides reference for the protection of wild roe deer.IMPORTANCEMany studies have shown that large and complex microbes in the gut of humans and non-human animals, intestinal microbes are thought to co-evolve with the host, help the host acquire nutrients, regulate immunity and to help maintain host homeostasis. The roe deer (Capreolus spp.) is a ruminant. Wild roe deer are listed on the List of Terrestrial Wild Animals Protected by the State or Have Important Economic and Scientific Values, wild roe deer is also a Chinese national protected animal under second class protection. However, current research on the gut microbiota of roe deer has not been reported.

Pollination Drop Proteome and Reproductive Organ Transcriptome Comparison in Gnetum Reveals Entomophilous Adaptation

Gnetum possesses morphologically bisexual but functionally unisexual reproductive structures that exude sugary pollination drops to attract insects. Previous studies have revealed that the arborescent species (G. gnemon L.) and the lianoid species (G. luofuense C.Y.Cheng) possess different pollination syndromes. This study compared the proteome in the pollination drops of these two species using label-free quantitative techniques. The transcriptomes of fertile reproductive units (FRUs) and sterile reproductive units (SRUs) for each species were furthermore compared using Illumina Hiseq sequencing, and integrated proteomic and transcriptomic analyses were subsequently performed. Our results show that the differentially expressed proteins between FRUs and SRUs were involved in carbohydrate metabolism, the biosynthesis of amino acids and ovule defense. In addition, the differentially expressed genes between the FRUs and SRUs (e.g., MADS-box genes) were engaged in reproductive development and the formation of pollination drops. The integrated protein-transcript analyses revealed that FRUs and their exudates were relatively conservative while the SRUs and their exudates were more diverse, probably functioning as pollinator attractants. The evolution of reproductive organs appears to be synchronized with changes in the pollination drop proteome of Gnetum, suggesting that insect-pollinated adaptations are not restricted to angiosperms but also occur in gymnosperms.

The mitochondrial genome and phylogenetic analysis of the tick Dermacentor everestianus Hirst, 1926 (Acari: Ixodidae)

The tick Dermacentor everestianus is widely distributed in Qinghai-Tibet Plateau of China and can transmit many zoonotic pathogens. In the current study, the complete mitochondrial (mt) genome of D. everestianus was sequenced through Illumina HiSeq sequencing. The mt genome is 15,191 bp in length which contains 37 genes, including 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. The overall GC content reached 21.20%, whereas the GC content in the gene region was 21.40%, and in the intergenetic region was 20.50%. Two control regions were sequenced from mt genome of D. everestianus, one located between tRNA-Cys and tRNA-Leu, and the other one was found between rrnS and tRNA-Ile. Two tandem repeats were found between tRNA-Glu and nad1. A phylogenetic tree was constructed based on the complete mitogenome of D. everestianus and 32 other ixodid tick mitogenomes to assess their phylogenetic relationships. D. everestianus is phylogenetically clustered with the tick D. silvarum and D. nuttalli. This is the first complete mt genome of D. everestianus, which provides a useful reference for future studies on systematics and population genetics of this tick species.

Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing

ABSTRACT Here, we report the first sequenced genome of an indigenous Australian wine isolate of Torulaspora delbrueckii using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.