Dataset Information

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus).

ABSTRACT:

Background

The loach (Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud environment.

Results

This study generated a 1.10-Gb high-quality, chromosome-anchored genome assembly, with a contig N50 of 3.83 Mb. Multiple comparative genomic analyses found that proto-oncogene c-Fos (fos), a regulator of bone development, is positively selected in loach. Knockout of fos (ID: Mis0086400.1) led to severe osteopetrosis and movement difficulties, combined with the comparison results of bone mineral density, supporting the hypothesis that fos is associated with loach mud-dwelling behavior. Based on genomic and transcriptomic analysis, we identified two key elements involved in the intestinal air-breathing of loach: a novel gene (ID: mis0158000.1) and heat shock protein beta-1 (hspb1). The flavin-containing monooxygenase 5 (fmo5) genes, central to xenobiotic metabolism, undergone expansion in loach and were identified as differentially expressed genes in a drug stress trial. A fmo5^-/- (ID: Mis0185930.1) loach displayed liver and intestine injury, indicating the importance of this gene to the adaptation of the loach to the noxious mud.

Conclusions

Our work provides valuable insights into the genetic basis of biological adaptation to adverse environments.

SUBMITTER: Sun B

PROVIDER: S-EPMC9893644 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus).

Sun Bing B Huang Yuwei Y Castro L Filipe C LFC Yang Su S Huang Songqian S Jin Wu W Zhou He H Ijiri Shigeho S Luo Yi Y Gao Jian J Cao Xiaojuan X

BMC biology 20230201 1

<h4>Background</h4>The loach (Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud ...[more]

PMID: 36726103

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Project description:Fish skin serves as the first line of defense against a wide variety of chemical, physical and biological stressors. Secretion of mucus is among the most prominent characteristics of fish skin and numerous innate immune factors have been identified in the epidermal mucus. However, molecular mechanisms underlying the mucus secretion and immune activities of fish skin remain largely unclear due to the lack of genomic and transcriptomic data for most economically important fish species. In this study, we characterized the skin transcriptome of mud loach using Illumia paired-end sequencing. A total of 40364 unigenes were assembled from 86.6 million (3.07 gigabases) filtered reads. The mean length, N50 size and maximum length of assembled transcripts were 387, 611 and 8670 bp, respectively. A total of 17336 (43.76%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. Gene ontology mapping assigned a total of 108513 GO terms to 15369 (38.08%) unigenes. KEGG orthology mapping annotated 9337 (23.23%) unigenes. Among the identified KO categories, immune system is the largest category that contains various components of multiple immune pathways such as chemokine signaling, leukocyte transendothelial migration and T cell receptor signaling, suggesting the complexity of immune mechanisms in fish skin. As for mucin biosynthesis, 37 unigenes were mapped to 7 enzymes of the mucin type O-glycan biosynthesis pathway and 8 members of the polypeptide N-acetylgalactosaminyltransferase family were identified. Additionally, 38 unigenes were mapped to 23 factors of the SNARE interactions in vesicular transport pathway, indicating that the activity of this pathway is required for the processes of epidermal mucus storage and release. Moreover, 1754 simple sequence repeats (SSRs) were detected in 1564 unigenes and dinucleotide repeats represented the most abundant type. These findings have laid the foundation for further understanding the secretary processes and immune functions of loach skin mucus.

Project description:BackgroundThe loach (Misgurnus anguillicaudatus) is a significant freshwater economic fish in China, renowned for its tender meat, delicious taste, and high nutritional value. It is widely distributed across the country, except for the western plateau. However, the loach is currently at risk of population decline and degradation of wildlife resources. Research on genetic diversity provides a crucial foundation for the conservation and development of these fish resources. To enhance the protection and utilization of wild loach germplasm resources, we analyzed the genetic structure and diversity of 60 wild loach populations from Xiangtan City (XT), Shaoyang City (SY), and Yueyang City (XY) in Hunan, Guilin City (GL) and Guiping City (GP) in Guangxi, and Wuhan City (WH) in Hubei. Additionally, we mapped the DNA fingerprints of these 60 wild loaches using 12 high-quality SNP sites.ResultsWhole genome resequencing (WGRS) was conducted on 60 loaches from six regions, yielding a total of 1047.17 Gb of raw data and 1046.98 Gb of clean data. From this 2,812,906 high-quality single nucleotide polymorphisms (SNPs) were identified, of which 10,022 core SNPs were selected to analyze the population genetic structure, and 12 core SNPs were used to assess the genetic diversity and DNA fingerprint. The analysis revealed that the 60 loach samples could be grouped into three clusters: Cluster A comprised the XT, SY, and XY groups; Cluster B included the WH group; and Cluster C consisted of the GL and GP groups. The mean nucleic acid diversity (Pi), heterozygosity (Ho), and expected heterozygosity (He) of SNP markers were 0.130, 0.140, and 0.123, respectively. The average inbreeding coefficient was 0.552, indicating high levels of inbreeding.ConclusionsWhole genome resequencing is an effective high-throughput approach for identifying SNP information in loach germplasm and describing genetic relationships within this genus. DNA fingerprinting based on SNP marker technology can accurately assess the genetic structure and variation within natural loach populations, making it a valuable tool for strain and variation identification. Our findings provide a scientific basis for the conservation, development, and optimal breeding of native loach germplasm resources and contribute to expanding the genetic diversity database of wild loach populations.

Dataset Information

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus).

Background

Results

Conclusions

Publications

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus).

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