Full-length transcriptome assembly of Andrias davidianus (Amphibia: Caudata) skin via hybrid sequencing

Transcriptomic analysis of liver immune response in Chinese spiny frog (Quasipaa spinosa) infected with Proteus mirabilis

The expansion of Chinese spiny frog (Quasipaa spinosa) aquaculture has increased the prevalence and severity of diseases such as "skin rot" disease, which is triggered by harmful bacteria. Previous studies have mainly focused on pathogen identification and vaccine development. However, frog immune responses following pathogenic bacterial infection have hardly been investigated. We thus examined the immune response of Chinese spiny frog to skin rot disease caused by Proteus mirabilis. The liver transcriptomes of Chinese spiny frog infected with P. mirabilis were sequenced using the MGISEQ-2000 platform. We identified a total of 138,936 unigenes, of which 32.35% were known genes. After infection with P. mirabilis, 801 genes showed differential expression, with 507 upregulated and 294 downregulated genes. These differentially expressed genes were enriched in pathways related to cytokine-cytokine receptor interaction, TNF signaling, and toll-like receptor signaling, according to Kyoto Encyclopedia of Genes and Genomes analysis. Following P. mirabilis infection, immune genes, including H2-Aa, hamp1, LYZ, CXCL10, and IRAK3, were significantly upregulated, while NLRP3, ADAM19, TYK2, FETUB, and MSR1 were significantly downregulated. The results provide important information on how the immune system of Chinese spiny frog responds to P. mirabilis infection and help understand the development of skin rot in cultured frog species.

Combined Analysis of Second- and Third-Generation Transcriptome Sequencing for Gene Characteristics and Identification of Key Splicing Variants in Wound Healing of Ganxi Goat Skin

Ganxi goat is a local breed of goat unique to Jiangxi Province, China, named for its primary distribution in the Ganxi region. Ganxi goats are primarily raised through grazing, showing good adaptation to the local humid and hot climate, strong disease resistance, and occupying an important position in the local livestock industry. The skin, as the main barrier of the body, plays an indispensable role in resisting the invasion of external pathogenic factors and has received increasing attention in the medical and scientific fields. In this study, Ganxi goat skin was used as the research subject. Full-length transcriptome sequencing of Ganxi goat skin was performed using PacBio third-generation sequencing technology to supplement and improve the annotation information of the Ganxi goat genome. A combined analysis of second- and third-generation transcriptome sequencing was used to analyze the splicing variant events of hub genes (CDC20, MMP2, TIMP1, and EDN1) and the expression changes in each splicing variant in skin samples on day 0 and day 5 after surgical wounding. The regulatory role of related hub gene splicing variants in wound healing was analyzed. A total of 926,667 full-length non-chimeric sequences were obtained, optimizing the annotation information of 3794 genomic gene loci and identifying 2834 new genes, 256 new LncRNAs, 12,283 alternative splicing events, 549 genes with polyadenylation, and 112 fusion genes. Three splicing variant forms were identified in both the CDC20 and EDN1 genes, seven in MMP2, and two in TIMP1. The expression levels of most splicing variants showed significant changes in the skin samples on days 0 and 5 after wounding, potentially participating in the regulation of wound healing. This study provides fundamental data for the annotation of the goat genome and offers a reference for studying the regulatory mechanisms of wound healing.

Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria

Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM ₍₁₎-trnL ₍₁₎-trnA-trnF-trnK-trnL ₍₂₎-trnQ-trnH-trnM ₍₂₎-nad2-nad3-atp9-cox2-trnR ₍₁₎-nad4L-nad5-cob-trnC-cox1-trnR ₍₂₎-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM ₍₃₎) was first processed from the mitogenome and was subsequently processed into smaller mono-, di-, or tricistronic RNAs.