1 Supplemental material 2 Genome sequencing of the perciform fish Larimichthys crocea 3 provides insights into stress adaptation 4 Jingqun Ao1†, Yinnan Mu1†, Li-Xin Xiang2†, DingDing Fan3†, MingJi Feng3†, Shicui Zhang4†, 5 Qiong Shi3, Lv-Yun Zhu2, Ting Li1, Yang Ding1, Li Nie2, Qiuhua Li1, Wei-ren Dong2, Liang 6 Jiang5, Bing Sun4, XinHui Zhang3, Mingyu Li1, Hai-Qi Zhang2, ShangBo Xie3, YaBing Zhu3, 7 XuanTing Jiang3, Xianhui Wang1, Pengfei Mu1, Wei Chen1, Zhen Yue3, Zhuo Wang3, Jun 8 Wang3*, Jian-Zhong Shao2* and Xinhua Chen1* 9 10 1 Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, 11 State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and 12 Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of 13 Fujian Province, Xiamen 361005, P.R. China 14 2 College of Life Sciences, ZheJiang University, Hangzhou 310058, ZheJiang, P.R. China 15 3 BGI-Tech, BGI-Shenzhen, Shenzhen 518083, Guangdong, P.R. China 16 4 Ocean University of China, Qingdao 266100, Shandong, P.R. China 17 5 College of Life Sciences, Shenzhen University, Shenzhen 518060, Guangdong, P.R. China 18 19 †These authors contributed equally to the work. 20 *To whom correspondence should be addressed: Xinhua Chen: Tel: +86-592-2195297, Fax: 21 +86-592-2195297, Email: [email protected]; Jun Wang: Tel: +86-755-25274247, Fax: 22 +86-755-25274247, Email: [email protected]; Jian-Zhong Shao: Tel: 23 +86-571-88206582, Fax: +86-571-88206582, Email: [email protected]. 24 25 Keywords: Large yellow croaker, Larimichthys crocea; Genome sequencing; Hypoxia; 26 Air exposure; Transcriptome; Proteome. 27 1 1 This PDF file includes 2 Supplemental Figures S1-S14 3 Supplemental Tables S1-S31 4 Supplemental notes 1-6 5 Supplemental references 1-45 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 2 1 Supplemental material 2 3 Supplemental Figures ................................................................................................................. 6 4 Supplemental Figure S1: Process of BAC and whole-genome shotgun (WGS) hierarchical 5 strategy ............................................................................................................................................................. 6 6 Supplemental Figure S2: Estimation of the L. crocea genome size based on K-mer analyses ..... 7 7 Supplemental Figure S3: Depth of single-base distribution based on short-read alignment.. ....... 8 8 Supplemental Figure S4: Distribution of intron length, exon number, mRNA length, exon 9 length, and coding region length in the genome of L. crocea and other related species. ............... 9 10 Supplemental Figure S5: Venn diagram representing the L. crocea gene models supported by 11 the ab initio prediction, homology-based methods, and RNAseq-based data. ............................... 10 12 Supplemental Figure S6: Phylogenetic analysis of crystallins in teleosts ....................................... 11 13 Supplemental Figure S7: Expansion of the olfactory receptor (OR) -like genes of “eta” group in 14 L. crocea genome ......................................................................................................................................... 12 15 Supplemental Figure S8: Expansion of tripartite motif-containing protein 25 (TRIM25) gene 16 family in L. crocea genome. ...................................................................................................................... 13 17 Supplemental Figure S9: Expansion of NOD-like receptor family CARD domain containing 3 18 (NLRC3) gene family in L. crocea genome ........................................................................................... 14 19 Supplemental Figure S10: Differentially expressed genes (DGEs) in the L. crocea brains under 20 hypoxic and normal conditions ................................................................................................................. 15 21 Supplemental Figure S11: Number of Differentially expressed genes (DGEs) at different time 22 points under hypoxia. .................................................................................................................................. 16 23 Supplemental Figure S12: The dynamic expression patterns of the genes involed in potential 24 nerve-endocrine-immunity network in the L. crocea brain under hypoxia. .................................... 17 25 Supplemental Figure S13: Expansion of the N-acetylgalactosaminyl transferase (GALNT) gene 26 family in L. crocea genome. ...................................................................................................................... 18 27 Supplemental Figure S14: Enrichment of Gene Ontology categories for skin mucus proteins. 19 28 29 Supplemental Tables ................................................................................................................. 20 30 Supplemental Table S1: Summary of BACs used in L. crocea genome project ............................ 20 3 1 Supplemental Table S2: Summary of k-mer analysis .......................................................................... 21 2 Supplemental Table S3: Stastics of BAC sequences used for mergence ......................................... 22 3 Supplemental Table S4: Information of whole-genome shotgun reads ............................................ 23 4 Supplemental Table S5: Statistics of final assembly ............................................................................ 24 5 Supplemental Table S6: Genome assembly validation by transcripts mapping ............................. 25 6 Supplemental Table S7: Summary of genome assembly of seven sequenced teleost species ..... 26 7 Supplemental Table S8: Summary of repetitive elements in L. crocea genome ............................ 27 8 Supplemental Table S9: Top ten transposable elements (TE) in seven teleost species ................. 28 9 Supplemental table S10: Comparison of repeat content from nine sequenced vetebrates ........... 29 10 Supplemental Table S11: Statistics of predicted protein-coding genes ............................................ 30 11 Supplemental Table S12: Functional classification of L. crocea genes by various methods ....... 31 12 Supplemental Table S13: Summary of gene families in the genomes of nine sequenced 13 vertebrate species by Treefam ................................................................................................................... 32 14 Supplemental Table S14: Gene Ontology of expanded gene families in the L. crocea genome . 33 15 Supplemental Table S15: Gene Ontology of contracted gene families in the L. crocea genome 35 16 Supplemental Table S16: Positive selection genes in the L. crocea genome .................................. 36 17 Supplemental Table S17: Copy number of vision-related genes in seven sequenced teleost 18 species ............................................................................................................................................................ 39 19 Supplemental Table S18: Olfactory receptor-like gene repertoire in seven sequenced teleost 20 species ............................................................................................................................................................ 40 21 Supplemental Table S19: Copy number of auditory sense-related genes in seven sequenced 22 teleost species ............................................................................................................................................... 41 23 Supplemental Table S20: Comparsion of the genes encoding for selenoproteins between L. 24 crocea and other sequenced vertebrate species ..................................................................................... 42 25 Supplemental Table S21: Characterization of the L. crocea immune system ................................. 44 26 Supplemental Table S22: Number of genes related to immunity in L. crocea and other six fish 27 genomes ......................................................................................................................................................... 45 28 Supplemental Table S23: Expression profiles of potential nerve-endocrine-immunity network- 29 related genes in the L. crocea brain under hypoxia .............................................................................. 46 30 Supplemental Table S24: Expression profiles of nerve-endocrine-metabolism network-related 4 1 genes in the L. crocea brain under hypoxia ............................................................................................ 47 2 Supplemental Table S25: Expression profiles of protein synthesis-related genes in the L. crocea 3 brain under hypoxia ..................................................................................................................................... 48 4 Supplemental Table S26: Genes involved in mucin biosynthesis and mucus production ............ 51 5 Supplemental Table S27: Summury of MS/MS spectra and identified proteins in the L. crocea 6 mucus under air exposure .......................................................................................................................... 53 7 Supplemental Table S28: Antioxidant proteins identified in the L. crocea mucus proteome ...... 54 8 Supplemental Table S29: Oxygen binding-related proteins identified in the L. crocea mucus 9 proteome .......................................................................................................................................................