Additional file 1 of The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus)
Creators: name: Sun, Bing
name: Huang, Yuwei
name: Castro, L. Filipe C.
name: Yang, Su
name: Huang, Songqian
name: Jin, Wu
name: Zhou, He
name: Ijiri, Shigeho
name: Luo, Yi
name: Gao, Jian
name: Cao, Xiaojuan
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Statistics of assembly and annotation of loach Misgurnus anguillicaudatus genome. (1) Statistics of Illumina HiSeq sequencing data of the loach genome. (2) 17-kmer analysis for estimation of the loach genome size. (3) Hi-C library sequencing data of the loach. (4) Statistics of repeated sequence classification of the loach genome. (5) Statistics of gene annotation of the loach genome. (6) Statistics of gene functional annotation of the loach genome. Table S2. Detailed gene information related to mud-dwelling behavior and intestinal evolution (air-breathing and digestion/absorption) of loach Misgurnus anguillicaudatus. (1) GO enrichment analysis of the expanded myosin complex genes in the loach genome. (2) KEGG enrichment analysis of the positively selected gene involved in osteoclast differentiation in the loach genome. (3) GO enrichment analysis of the expanded gene families involved in oxygen transport in the loach genome. Red and black gene IDs present hbb and hba genes, respectively. (4) KEGG enrichment analysis of the positively selected genes involved in VEGF signaling pathway in the loach genome. (5) Expression analysis of some DEGs in posterior intestine transcriptomes between Leptobotia elongate (LE, without air-breathing) and the loach (MA, with intestinal air-breathing) (referred from our previous study). (6) Summary of detected microRNAs and target genes involved in vascular biology of loach posterior intestines (referred from our previous study). (7) The DEGs involved in intestinal air-breathing and nutrient uptake of the loach (referred from our previous studies) (8) Expression analysis of five key DEGs in posterior intestine transcriptomes of the loach between the control (C_chang) and air exposure (T_chang) group. Un means Mis0158000.1, which is a new gene and its KEGG annotation is interleukin 1 beta (Il1b). (9) KEGG enrichment analysis of the contracted gene families involved in digestion/absorption of the loach. (10) KEGG enrichment analysis of the expanded genes involved in digestion/absorption of the loach. hbb, hemoglobin subunit beta; hba, hemoglobin subunit alpha; VEGF, vascular endothelial growth factor; DEGs, differentially expressed genes; Il1b, Interleukin-1 beta; cldn5, Claudin-5 Transmembrane protein deleted in VCFS; hspb1, heat shock protein beta-1; vegfr1 (flt1), vascular endothelial growth factor receptor1; ctgf, Connective tissue growth factor CCN family member 2; hif1a, hypoxia-inducible factor 1-alpha. Table S3. Genes involved in detoxification function of loach Misgurnus anguillicaudatus. (1) The expanded genes involved in the detoxification function of the loach genome. (2) KEGG enrichment analysis of DEGs involved in the xenobiotics biodegradation and metabolism between the control and five drug stress groups. Red and black gene IDs present fmo and ugt genes, respectively. DEGs, differentially expressed genes. Table S4. Gene annotations for the zebrafish gene clusters in this study. Fos, proto-oncogene c-Fos; hba, hemoglobin subunit alpha; hbb, hemoglobin subunit beta; ryr, ryanodine receptor; atp1a, sodium/potassium-transporting ATPase subunit alpha; cldn5, claudin-5; vegfr1, vascular endothelial growth factor receptor 1; hspb1, heat shock protein beta-1; ctgf, connective tissue growth factor CCN family member 2; fmo, dimethylaniline monooxygenase [N-oxide-forming]; ugt, UDP-glucuronosyltransferase. Table S5. Primers used in this study. qPCR, quantitative PCR; # indicated T7 promoter sequences. Fos, proto-oncogene c-Fos; fmo5, dimethylaniline monooxygenase [N-oxide-forming] 5 (Mis0185930.1); hbb, hemoglobin subunit beta; hba, hemoglobin subunit alpha; atf6, cyclic AMP-dependent transcription factor; eif2ak3, eukaryotic translation initiation factor 2-alpha kinase 3; chop, DNA damage-inducible transcript 3 protein; muc2, mucin-2; Mis0185950.1, Mis0185940.1, Mis0185920.1, Mis0185970.1, Mis0186000.1, Mis0186010.1 (fmo5), dimethylaniline monooxygenase [N-oxide-forming] 5; Mis0115330.1, Mis0115330.1, Mis0135560.1 (ugt2a2), UDP-glucuronosyltransferase 2A2; Mis0072610.1 (ugt2a1), UDP-glucuronosyltransferase 2A1; npr2, atrial natriuretic peptide receptor 2; f9, coagulation factor IX; hspb1, heat shock protein beta-1; hyou1, hypoxia up-regulated protein 1; ptafr, platelet-activating factor receptor; scx, basic helix-loop-helix transcription factor scleraxis; galnt8, polypeptide N-acetylgalactosaminyltransferase 8; krt13, keratin, type I cytoskeletal 13 Cytokeratin-13; gp2, pancreatic secretory granule membrane major glycoprotein; smco3, single-pass membrane and coiled-coil domain-containing protein 3; ccl5, C-C motif chemokine 5; ifi44, interferon-induced protein 44; atf4, cyclic AMP-dependent transcription factor 4; ugt1a1, UDP-glucuronosyltransferase 1-1. Table S6. A summary of sequencing data used in genome assembly and annotation of Misgurnus anguillicaudatus.