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Zhao X, Zheng T, Gao T, Song N. Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations. BMC Genomics 2023; 24:547. [PMID: 37715145 PMCID: PMC10503073 DOI: 10.1186/s12864-023-09652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. RESULTS To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. CONCLUSIONS Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China
| | - Tianlun Zheng
- Zhejiang Fisheries Technical Extension Center, Hangzhou, 310023, Zhejiang, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China.
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2
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Han X, Jin S, Han Z, Gao T. The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis. Animals (Basel) 2022; 12:ani12233386. [PMID: 36496907 PMCID: PMC9741161 DOI: 10.3390/ani12233386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic−Indo−West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic−Indo−West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.
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Zhang Y, Lou F, Chen J, Han Z, Yang T, Gao T, Song N. Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1002-1013. [PMID: 36083383 DOI: 10.1007/s10126-022-10163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.
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Affiliation(s)
- Yuan Zhang
- Fishery College, Ocean University of China, Qingdao, 266003, China
| | - Fangrui Lou
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Na Song
- Fishery College, Ocean University of China, Qingdao, 266003, China.
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4
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Li Z, Wang J, Fu Y, Jing Y, Huang B, Chen Y, Wang Q, Wang XB, Meng C, Yang Q, Xu L. The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids. BMC Biol 2022; 20:186. [PMID: 36002843 PMCID: PMC9400310 DOI: 10.1186/s12915-022-01391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/15/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Karat (Musa troglodytarum L.) is an autotriploid Fe'i banana of the Australimusa section. Karat was domesticated independently in the Pacific region, and karat fruit are characterized by a pink sap, a deep yellow-orange flesh colour, and an abundance of β-carotene. Karat fruit showed non-climacteric behaviour, with an approximately 215-day bunch filling time. These features make karat a valuable genetic resource for studying the mechanisms underlying fruit development and ripening and carotenoid biosynthesis. RESULTS Here, we report the genome of M. troglodytarum, which has a total length of 603 Mb and contains 37,577 predicted protein-coding genes. After divergence from the most recent common ancestors, M. troglodytarum (T genome) has experienced fusion of ancestral chromosomes 8 and 9 and multiple translocations and inversions, unlike the high synteny with few rearrangements found among M. schizocarpa (S genome), M. acuminata (A genome) and M. balbisiana (B genome). Genome microsynteny analysis showed that the triplication of MtSSUIIs due to chromosome rearrangement may lead to the accumulation of carotenoids and ABA in the fruit. The expression of duplicated MtCCD4s is repressed during ripening, leading to the accumulation of α-carotene, β-carotene and phytoene. Due to a long terminal repeat (LTR)-like fragment insertion upstream of MtERF11, karat cannot produce large amounts of ethylene but can produce ABA during ripening. These lead to non-climacteric behaviour and prolonged shelf-life, which contributes to an enrichment of carotenoids and riboflavin. CONCLUSIONS The high-quality genome of M. troglodytarum revealed the genomic basis of non-climacteric behaviour and enrichment of carotenoids, riboflavin, flavonoids and free galactose and provides valuable resources for further research on banana domestication and breeding and the improvement of nutritional and bioactive qualities.
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Affiliation(s)
- Zhiying Li
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Jiabin Wang
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Yunliu Fu
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Yonglin Jing
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Bilan Huang
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Ying Chen
- grid.428986.90000 0001 0373 6302College of Horticulture and Landscape Architecture, Hainan University, Haikou, 570228 China
| | - Qinglong Wang
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China
| | - Xiao Bing Wang
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Chunyang Meng
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Qingquan Yang
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
| | - Li Xu
- grid.453499.60000 0000 9835 1415Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China ,Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Danzhou, 571737 Hainan China ,Hainan Province Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation, Danzhou, 571737 Hainan China ,National Gene Bank of Tropical Crops, Danzhou, 571700 Hainan China
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5
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Yang T, Ning Z, Liu Y, Zhang S, Gao T. Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform. Biosci Rep 2022; 42:BSR20220460. [PMID: 35502704 PMCID: PMC9142832 DOI: 10.1042/bsr20220460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Ophichthidae fishes limit to continental shelf of all tropical and subtropical oceans and contain more than 350 species, representing the greatest specialization diversity in the order Anguiliformes. In the present study, we conducted a genome survey sequencing (GSS) analysis of Ophichthus evermanni by Illumina sequencing platform to briefly reveal its genomic characteristics and phylogenetic relationship. The first de novo assembled 1.97 Gb draft genome of O. evermanni was predicted based on K-mer analysis without obvious nucleotide bias. The heterozygosity ratio was 0.70%, and the sequence repeat ratio was calculated to be 43.30%. A total of 9016 putative coding genes were successfully predicted, in which 3587 unigenes were identified by gene ontology (GO) analysis and 4375 unigenes were classified into cluster of orthologous groups for enkaryotic complete genomes (KOG) functional categories. About 2,812,813 microsatellite motifs including mono-, di-, tri-, tetra-, penta- and hexanucleotide motifs were identified, with an occurrence frequency of 23.32%. The most abundant type was dinucleotide repeat motifs, accounting for 49.19% of the total repeat types. The mitochondrial genome, as a byproduct of GSS, was assembled to investigate the evolutionary relationships between O. evermanni and its relatives. Bayesian inference (BI) phylogenetic tree inferring from concatenated 12 protein-coding genes (PCGs) showed complicated relationships among Ophichthidae species, indicating a polyphyletic origin of the family. The results would achieve more thorough genetic information of snake eels and provide a theoretical basis and reference for further genome-wide analysis of O. evermanni.
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Affiliation(s)
- Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zijun Ning
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yuping Liu
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
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6
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Yu H, Zhang L, Shang X, Peng B, Li Y, Xiao S, Tan Q, Fu Y. Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes. BMC Genomics 2022; 23:120. [PMID: 35144543 PMCID: PMC8832684 DOI: 10.1186/s12864-022-08325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses. RESULTS A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress. CONCLUSIONS A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.
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Affiliation(s)
- Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Yu Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, 314000, China.
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China.
| | - Yongping Fu
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
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7
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Comparative genomic analysis of different sexes and diet-specific amino acid mutation identification in Ancherythroculter nigrocauda. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100910. [PMID: 34509952 DOI: 10.1016/j.cbd.2021.100910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/27/2023]
Abstract
Determining the sex and controlling the sex ratio are essential aspects of fish genetics that can assist in developing successful fish breeding programs. High quality genome assembly and annotations are prerequisites to determine sex-specific genes and their expression. In addition, analysis of resequencing data can identify genomic difference between male and female fishes. In this study, we performed chromosome-level genome assembly in female Ancherythroculter nigrocauda fish having low heterozygosity using PacBio reads. High-throughput chromatin conformation capture (HiC) yielded a genome of size 1054.05 Mb, with a contig N50 length of 3.40 Mb and a scaffold N50 length of 42.68 Mb. In addition, we sequenced 5 female and 5 male A. nigrocauda samples and identified sex-specific regions on LG20 Furthermore, diet-specific amino acid mutation were found on 582 genes between herbivorous and carnivorous fishes, with 26 of them exhibiting significantly different expression patterns in the liver tissue of these two types of fishes. The chromosome-level genome assembly of A. nigrocauda provides valuable resources for conducting in-depth comparative genomic studies with immense applications in fish genetic breeding and farming. Similarly, the diet-specific amino acid mutations are useful in the breeding of new strains of carnivorous fishes with an herbivorous diet.
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8
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Huang C, Ying H, Yang X, Gao Y, Li T, Wu B, Ren M, Zhang Z, Ding J, Gao J, Wen D, Ye X, Liu L, Wang H, Sun G, Zou Y, Chen N, Wang L. The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance. Cell Discov 2021; 7:62. [PMID: 34373445 PMCID: PMC8352907 DOI: 10.1038/s41421-021-00286-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Cardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited. Here, we report a chromosome-level genome assembly of C. enshiensis, which consists of 443.4 Mb in 16 chromosomes with a scaffold N50 of 24 Mb. To elucidate the mechanism of Se tolerance and hyperaccumulation in C. enshiensis, we generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes. The results reveal that flavonoid, glutathione, and lignin biosynthetic pathways may play important roles in protecting C. enshiensis from stress induced by Se. Hi-C analysis of chromatin interaction patterns showed that the chromatin of C. enshiensis is partitioned into A and B compartments, and strong interactions between the two telomeres of each chromosome were correlated with histone modifications, epigenetic markers, DNA methylation, and RNA abundance. Se supplementation could affect the 3D chromatin architecture of C. enshiensis at the compartment level. Genes with compartment changes after Se treatment were involved in selenocompound metabolism, and genes in regions with topologically associated domain insulation participated in cellular responses to Se, Se binding, and flavonoid biosynthesis. This multiomics research provides molecular insight into the mechanism underlying Se tolerance and hyperaccumulation in C. enshiensis.
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Affiliation(s)
- Chuying Huang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China. .,Hubei Selenium and Human Health Institute, Enshi, Hubei, China.
| | - Hongqin Ying
- Hubei Selenium Industrial Technology Research Institute, Enshi Autonomous Prefecture Academy of Agriculture Sciences, Enshi, Hubei, China
| | - Xibiao Yang
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yuan Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30, Gothenburg, Sweden
| | - Tuo Li
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Bo Wu
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Meng Ren
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zixiong Zhang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Jun Ding
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Jianhua Gao
- South China Potato Research Center, Enshi Autonomous Prefecture Academy of Agricultural Sciences, Enshi, Hubei, China
| | - Dan Wen
- Bureau of Agricultural & Rural Affairs of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Xingzhi Ye
- South China Potato Research Center, Enshi Autonomous Prefecture Academy of Agricultural Sciences, Enshi, Hubei, China
| | - Ling Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Guogen Sun
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Yi Zou
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
| | - Nansheng Chen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Li Wang
- Hubei Minzu University Affiliated Enshi Clinical Medical School, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China.,Hubei Selenium and Human Health Institute, Enshi, Hubei, China
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9
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Xu T, Li Y, Chu Q, Zheng W. A chromosome-level genome assembly of the red drum, Sciaenops ocellatus. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Lin X, Huang Y, Jiang D, Chen H, Deng S, Zhang Y, Du T, Zhu C, Li G, Tian C. Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama). Genome Biol Evol 2021; 13:evaa272. [PMID: 33367716 PMCID: PMC7875006 DOI: 10.1093/gbe/evaa272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of Sillago sinica ∼7.92 Ma. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.
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Affiliation(s)
- Xinghua Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yang Huang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Dongneng Jiang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Huapu Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Siping Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yulei Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Tao Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Chunhua Zhu
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Guangli Li
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Changxu Tian
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
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11
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Wang L, Zhu P, Mo Q, Luo W, Du Z, Jiang J, Yang S, Zhao L, Gong Q, Wang Y. Comprehensive analysis of full-length transcriptomes of Schizothorax prenanti by single-molecule long-read sequencing. Genomics 2021; 114:456-464. [PMID: 33516848 DOI: 10.1016/j.ygeno.2021.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Schizothorax prenanti (S. prenanti) is one of the most important aquaculture species in the southwest of China. However, information of the full-length transcripts in S. prenanti remains unknown. In this study, single-molecule real-time (SMRT) sequencing was performed to generate full-length transcriptomes of S.prenanti. In total, 23.26 Gb of clean reads were generated. A total of 312,587 circular consensus sequences (CCS) were obtained with average lengths of 2634 bp and 84.16% (270,662) of CCS were full-length non-chimeric reads. After being corrected with Illumina library sequencing, 18,005 contigs were obtained, with 17,797 (98.81%) successfully annotated in eight public databases, including 15,839 complete open reading frames (ORFs) with an average length of 1330 bp. Furthermore, a total of 4152 alternative splicing (AS) events and 250 long non-coding RNA (lncRNA) transcripts were detected. Additionally, a total of 1129 putative transcription factors (TFs) members from 56 TF families and 11,660 simple sequence repeats (SSRs) were identified. This study provided a valuable resource of full-length transcripts for further research on S. prenanti.
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Affiliation(s)
- Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Peng Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Qilang Mo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Quan Gong
- Fisheries institute, Sichuan Academy of Agricultural Sciences, Chengdu 611713, Sichuan, PR China
| | - Yan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China.
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12
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Qu Z, Nong W, Yu Y, Baril T, Yip HY, Hayward A, Hui JHL. Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae). BMC Genomics 2020; 21:726. [PMID: 33076831 PMCID: PMC7574432 DOI: 10.1186/s12864-020-07145-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/12/2020] [Indexed: 12/02/2022] Open
Abstract
Background Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae. Results We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. Conclusions The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07145-1.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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13
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Liang P, Saqib HSA, Ni X, Shen Y. Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 2020; 21:640. [PMID: 32938378 PMCID: PMC7493909 DOI: 10.1186/s12864-020-07042-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/31/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. RESULTS In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. CONCLUSIONS The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.
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Affiliation(s)
- Pingping Liang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hafiz Sohaib Ahmed Saqib
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomin Ni
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
- Fudan University, Shanghai, 200240, China
| | - Yingjia Shen
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
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14
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Lou F, Zhang Y, Song N, Ji D, Gao T. Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species. Animals (Basel) 2020; 10:ani10040633. [PMID: 32272562 PMCID: PMC7222750 DOI: 10.3390/ani10040633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023] Open
Abstract
Sillago species lives in the demersal environments and face multiple stressors, such as localized oxygen depletion, sulfide accumulation, and high turbidity. In this study, we performed transcriptome analyses of seven Sillago species to provide insights into the phylogeny and positively selected genes of this species. After de novo assembly, 82,024, 58,102, 63,807, 85,990, 102,185, 69,748, and 102,903 unigenes were generated from S. japonica, S. aeolus, S. sp.1, S. sihama, S. sp.2, S. parvisquamis, and S. sinica, respectively. Furthermore, 140 shared orthologous exon markers were identified and then applied to reconstruct the phylogenetic relationships of the seven Sillago species. The reconstructed phylogenetic structure was significantly congruent with the prevailing morphological and molecular biological view of Sillago species relationships. In addition, a total of 44 genes were identified to be positively selected, and these genes were potential participants in the stress response, material (carbohydrate, amino acid and lipid) and energy metabolism, growth and differentiation, embryogenesis, visual sense, and other biological processes. We suspected that these genes possibly allowed Sillago species to increase their ecological adaptation to multiple environmental stressors.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China;
| | - Yuan Zhang
- Fishery College, Ocean University of China, Qingdao 266003, Shandong, China; (Y.Z.); (N.S.)
| | - Na Song
- Fishery College, Ocean University of China, Qingdao 266003, Shandong, China; (Y.Z.); (N.S.)
| | - Dongping Ji
- Agricultural Machinery Service Center, Fangchenggang 538000, Guangxi, China;
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China;
- Correspondence: ; Tel.: +86-580-2089-333
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15
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Qiu B, Fang S, Ikhwanuddin M, Wong L, Ma H. Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology. Mol Biol Rep 2020; 47:3011-3017. [PMID: 32124169 DOI: 10.1007/s11033-020-05348-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we first conducted a genome survey assay for Sillago sihama by Illumina sequencing platform, and then developed 15 polymorphic microsatellite loci in a wild population. A total of 129.46 Gb raw data were obtained, of which 115.07 Gb were clean data, with a sequencing depth of 179.3-folds. This genome was estimated to be 522.6 Mb in size, with the heterozygosity, repeat content and GC content being 0.63%, 21% and 44%. A total of 630,028 microsatellites were identified from the genome, of which, dinucleotide repeat was the most abundant (56.80%), followed by mononucleotide repeat (30.23%). Furthermore, 60 pairs of primers were designed and synthesized based on microsatellite sequences, of which 15 were polymorphic in a wild population. A total of 91 alleles were found, with an average of 6.07 per locus. Number of alleles, observed and expected heterozygosity per locus ranged from two to 13, from 0.250 to 0.862, and from 0.396 to 0.901, respectively. Twelve loci were highly informative (PIC > 0.5), and the others were medium informative (0.25 < PIC < 0.5). Seven loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0033). No significant linkage disequilibrium was detected between loci pairs. This study provided a large number of genomic resources and 15 polymorphic microsatellite loci that should be helpful for the further genetic studies in S. sihama.
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Affiliation(s)
- Bixun Qiu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Lilian Wong
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China. .,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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Genome Survey of Male and Female Spotted Scat ( Scatophagus argus). Animals (Basel) 2019; 9:ani9121117. [PMID: 31835725 PMCID: PMC6940847 DOI: 10.3390/ani9121117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus. Abstract The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.
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Zhou Y, Xiao S, Lin G, Chen D, Cen W, Xue T, Liu Z, Zhong J, Chen Y, Xiao Y, Chen J, Guo Y, Chen Y, Zhang Y, Hu X, Huang Z. Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data. Sci Data 2019; 6:267. [PMID: 31704938 PMCID: PMC6841922 DOI: 10.1038/s41597-019-0279-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/18/2019] [Indexed: 01/18/2023] Open
Abstract
Pufferfish are ideal models for vertebrate chromosome evolution studies. The yellowbelly pufferfish, Takifugu flavidus, is an important marine fish species in the aquaculture industry and ecology of East Asia. The chromosome assembly of the species could facilitate the study of chromosome evolution and functional gene mapping. To this end, 44, 27 and 50 Gb reads were generated for genome assembly using Illumina, PacBio and Hi-C sequencing technologies, respectively. More than 13 Gb full-length transcripts were sequenced on the PacBio platform. A 366 Mb genome was obtained with the contig of 4.4 Mb and scaffold N50 length of 15.7 Mb. 266 contigs were reliably assembled into 22 chromosomes, representing 95.9% of the total genome. A total of 29,416 protein-coding genes were predicted and 28,071 genes were functionally annotated. More than 97.7% of the BUSCO genes were successfully detected in the genome. The genome resource in this work will be used for the conservation and population genetics of the yellowbelly pufferfish, as well as in vertebrate chromosome evolution studies.
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Affiliation(s)
- Yitao Zhou
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China
| | - Gang Lin
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, Fujian Normal University, Fuzhou, Fujian, China
| | - Duo Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Wan Cen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Ting Xue
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Zhiyu Liu
- Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Jianxing Zhong
- Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Yanting Chen
- Fujian Fishery Technical Extension Center, Fuzhou, Fujian, China
| | - Yijun Xiao
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Jianhua Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Yanding Zhang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xuefeng Hu
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China.
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China.
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Zhang X, Zhang X, Song N, Gao T, Zhao L. Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:825-834. [PMID: 31571512 DOI: 10.1080/24701394.2019.1670820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.
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Affiliation(s)
- Xiaomeng Zhang
- Fisheries College, Ocean University of China, Qingdao, China
| | - Xiumei Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.,Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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Li Z, Tian C, Huang Y, Lin X, Wang Y, Jiang D, Zhu C, Chen H, Li G. A First Insight into a Draft Genome of Silver Sillago ( Sillago sihama) via Genome Survey Sequencing. Animals (Basel) 2019; 9:ani9100756. [PMID: 31581597 PMCID: PMC6827152 DOI: 10.3390/ani9100756] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022] Open
Abstract
Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).
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Affiliation(s)
- Zhiyuan Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Changxu Tian
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
| | - Yang Huang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
| | - Xinghua Lin
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Yaorong Wang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Dongneng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
| | - Chunhua Zhu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
| | - Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China.
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20
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Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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21
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Liu Q, Guo Y, Zhang Y, Hu W, Li Y, Zhu D, Zhou Z, Wu J, Chen N, Zhou XN. A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. Gigascience 2019; 8:giz089. [PMID: 31425588 PMCID: PMC6699579 DOI: 10.1093/gigascience/giz089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/06/2019] [Accepted: 07/02/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Triatoma rubrofasciata is a widespread pathogen vector for Chagas disease, an illness that affects approximately 7 million people worldwide. Despite its importance to human health, its evolutionary origin has not been conclusively determined. A reference genome for T. rubrofasciata is not yet available. FINDING We have sequenced the genome of a female individual with T. rubrofasciatausing a single molecular DNA sequencing technology (i.e., PacBio Sequel platform) and have successfully reconstructed a whole-genome (680-Mb) assembly that covers 90% of the nuclear genome (757 Mb). Through Hi-C analysis, we have reconstructed full-length chromosomes of this female individual that has 13 unique chromosomes (2n = 24 = 22 + X1 + X2) with a contig N50 of 2.72 Mb and a scaffold N50 of 50.7 Mb. This genome has achieved a high base-level accuracy of 99.99%. This platinum-grade genome assembly has 12,691 annotated protein-coding genes. More than 95.1% of BUSCO genes were single-copy completed, indicating a high level of completeness of the genome. CONCLUSION The platinum-grade genome assembly and its annotation provide valuable information for future in-depth comparative genomics studies, including sexual determination analysis in T. rubrofasciata and the pathogenesis of Chagas disease.
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Affiliation(s)
- Qin Liu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan, Shanghai 200025, P. R. China
| | - Yuanyuan Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Dan Zhu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Zhengbin Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Jiatong Wu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, P. R. China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, P. R. China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Center for Tropical Diseases; Chinese Center for Tropical Diseases Research, Shanghai 200025, P. R. China
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22
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Cai M, Zou Y, Xiao S, Li W, Han Z, Han F, Xiao J, Liu F, Wang Z. Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. Sci Data 2019; 6:132. [PMID: 31341172 PMCID: PMC6656731 DOI: 10.1038/s41597-019-0139-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Collichthys lucidus (C. lucidus) is a commercially important marine fish species distributed in coastal regions of East Asia with the X1X1X2X2/X1X2Y multiple sex chromosome system. The karyotype for female C. lucidus is 2n = 48, while 2n = 47 for male ones. Therefore, C. lucidus is also an excellent model to investigate teleost sex-determination and sex chromosome evolution. We reported the first chromosome genome assembly of C. lucidus using Illumina short-read, PacBio long-read sequencing and Hi-C technology. An 877 Mb genome was obtained with a contig and scaffold N50 of 1.1 Mb and 35.9 Mb, respectively. More than 97% BUSCOs genes were identified in the C. lucidus genome and 28,602 genes were annotated. We identified potential sex-determination genes along chromosomes and found that the chromosome 1 might be involved in the formation of Y specific metacentric chromosome. The first C. lucidus chromosome-level reference genome lays a solid foundation for the following population genetics study, functional gene mapping of important economic traits, sex-determination and sex chromosome evolution studies for Sciaenidae and teleosts. Design Type(s) | sequence assembly objective • sequence annotation objective • transcription profiling design | Measurement Type(s) | whole genome sequencing assay • transcript expression assay | Technology Type(s) | DNA sequencing • RNA sequencing | Factor Type(s) | organism part | Sample Characteristic(s) | Collichthys lucidus |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China.
| | - Yu Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China.,Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Junzhu Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Fujiang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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23
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Xu S, Zhao L, Xiao S, Gao T. Whole genome resequencing data for three rockfish species of Sebastes. Sci Data 2019; 6:97. [PMID: 31222011 PMCID: PMC6586840 DOI: 10.1038/s41597-019-0100-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023] Open
Abstract
Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43 Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1 Mb and the sequencing coverages were 45×, 49×, and 46× for three rockfish, respectively. Comparative genomic analyses identified 46,624 genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed closer relationships of the three species, compared to other six rockfish species. Demographic analysis identified contrasting changes between S. schlegelii and other two species, suggesting drastically different response to climate changes. The reported genome data in this study are valuable for further studies on comparative genomics and evolutionary biology of rockfish species. Design Type(s) | species comparison design • sequence analysis objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Sebastes schlegelii • Sebastes koreanus • Sebastes nudus |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Shengyong Xu
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China
| | - Linlin Zhao
- The First Institute of Oceanography, Ministry of Natural Resources, 6th Xianxialing Road, Qingdao, 266061, P.R. China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, 122th Luoshi Road, Wuhan, 430070, P.R. China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
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24
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Tian C, Li Z, Dong Z, Huang Y, Du T, Chen H, Jiang D, Deng S, Zhang Y, Wanida S, Shi H, Wu T, Zhu C, Li G. Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago ( Sillago sihama). Genes (Basel) 2019; 10:E129. [PMID: 30754713 PMCID: PMC6409516 DOI: 10.3390/genes10020129] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 01/14/2023] Open
Abstract
Silver sillago (Sillago sihama) is an emerging commercial marine aquaculture species in China. To date, fundamental information on S. sihama, such as genomic information, is lacking, and no data are available on the gonad transcriptome of S. sihama. Here, the first gonadal transcriptomes of S. sihama have been constructed and genes potentially involved in gonadal development and reproduction identified. Illumina sequencing generated 60.18 million clean reads for the testis and 59.10 million for the ovary. All reads were assembled into 74,038 unigenes with a mean length of 1,004 bp and N50 value of 2,190 bp. Among all the predictable unigenes, a total of 34,104 unigenes (46%) were searched against multiple databases, including 33,244 unigenes annotated in the RefSeq Non- Redundant database at NCBI, and 28,924 in Swiss-Prot. By comparing the ovary and testis, 35,367 unigenes were identified as being differentially expressed between males and females, of which 29,127 were upregulated in the testis and 6,240 were upregulated in the ovary. Numerous differentially expressed genes (DEGs) known to be involved in gonadal development and gametogenesis were identified, including amh, dmrt1, gsdf, cyp19a1a, gnrhr, and zps. Using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, the top 20 KEGG pathways with highest number of DEGs were found to be involved in regulating gonadal development and gametogenesis in S. sihama. Moreover, 22,666 simple sequence repeats (SSRs) were identified in 14,577 SSR-containing sequences. The findings provide a valuable dataset for future functional analyses of sex-associated genes and molecular marker assisted selection in S. sihama.
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Affiliation(s)
- Changxu Tian
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Zhiyuan Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Zhongdian Dong
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Yang Huang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Tao Du
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Dongneng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Siping Deng
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Yulei Zhang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Saetan Wanida
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Hongjuan Shi
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Tianli Wu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Chunhua Zhu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
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25
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Zhang S, Li J, Qin Q, Liu W, Bian C, Yi Y, Wang M, Zhong L, You X, Tang S, Liu Y, Huang Y, Gu R, Xu J, Bian W, Shi Q, Chen X. Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes. Toxins (Basel) 2018; 10:E488. [PMID: 30477130 PMCID: PMC6316204 DOI: 10.3390/toxins10120488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 11/18/2022] Open
Abstract
Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.
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Affiliation(s)
- Shiyong Zhang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Jia Li
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
| | - Qin Qin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Wei Liu
- Nanjing Institute of Fisheries Science, Nanjing 210029, China.
| | - Chao Bian
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
| | - Yunhai Yi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
| | - Minghua Wang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Liqiang Zhong
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Xinxin You
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
| | - Shengkai Tang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Yanshan Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Yu Huang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
| | - Ruobo Gu
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
| | - Junmin Xu
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Wenji Bian
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
| | - Xiaohui Chen
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.
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Xu S, Xiao S, Zhu S, Zeng X, Luo J, Liu J, Gao T, Chen N. A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. Gigascience 2018; 7:5094561. [PMID: 30202912 PMCID: PMC6143730 DOI: 10.1093/gigascience/giy108] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/21/2018] [Accepted: 08/21/2018] [Indexed: 11/15/2022] Open
Abstract
Background Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family. Findings Using the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago. Conclusions Using long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.
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Affiliation(s)
- Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang316022, China
| | - Shijun Xiao
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Shilin Zhu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Xiaofei Zeng
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Jing Luo
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Jiaqi Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang316022, China
| | - Nansheng Chen
- CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
- Laboratoryfor Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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