Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

Fan, Guanngyi; Song, Yue; Huang, Xiaoyun; Yang, Liandong; Zhang, Suyu; Zhang, Mengqi; Chang, Yue; Zhang, He; Li, Yongxin; Liu, Shanshan; Yu, Lili; Seim, Inge; Feng, Chenguang; Wang, Wen; Wang, Kun; Wang, Jing; Xu, Xun; Yang, Huanming; Chen, Nansheng; Liu, Xin; He, Shunping

doi:10.1101/787028

Cited by 14 publications

(19 citation statements)

References 12 publications

(13 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Compared with other species (mammal, bird, bony fish, and cartilaginous fish), the genome size of smelt is smaller than that of other species, but the GC content of genome and coding sequence (CDS) and GC content of CDS are similar to those of other species, and the number of CDS is even more than that of other species (Supplementary Table S15). The genome size of H. nipponensis is within the range of most published fish genome sizes ( Fan et al 2020 ).…”

Section: Discussionmentioning

confidence: 74%

Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

Xuan

Park

Choi

et al. 2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5 °C) versus warm (HT, 23 °C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO : 0008610, P < 0.001) and regulation of apoptotic process (GO : 0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO : 0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO : 0001666, P < 0.05), transcription regulator activity (GO : 0140110, P < 0.001) and calcium-release channel activity (GO : 0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO : 0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

show abstract

Section: Discussionmentioning

confidence: 74%

Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

Xuan

Park

Choi

et al. 2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…Molecular biological experiments such as RNAi, gene knockout or genetic modification to verify the genetic mechanism underpinning the diet transition are also needed. Moreover, the additional de novo genomic researches and comparative genomic researches on Osteoglossidae and other Osteoglossiformes fish, which will help us to understand the evolution of this ancient teleost clade such as 10000 fish genome project (Fish10K) ( Fan et al., 2020 ). The resequencing genomic and ancient genomic studies about these three Osteoglossiformes fishes were required to disclose the population structure, migration history, and genomic changes in their own genome along with the time.…”

Section: Discussionmentioning

confidence: 99%

African Arowana Genome Provides Insights on Ancient Teleost Evolution

Hao¹,

Han²,

Meng³

et al. 2020

iScience

Self Cite

View full text Add to dashboard Cite

Summary Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution.

show abstract

“…All genome projects have a common but monumental goal: sequencing the entire target genome for a wide range of genomics applications. While genomics is a rich field, one of the most prominent scientific objectives is probably securing the future of sustainable food sources by harnessing the power of genomics (i.e., desirable traits) [19][20][21][23][24][25], particularly for agriculture. If the species of interest is distinct from the wild, cultured, or harvested, it necessitates networking and building a scientific or stakeholder community to support the project.…”

Section: Step 1: Build a Wide Community For The Project If Possiblementioning

confidence: 99%

“…Given that aquaculture is the most rapidly expanding food sector, with the widest diversity of species cultured, it is poised for rapid adoption of genomics applications as these become more accessible. For any specific advice on application of genomics to aquaculture, please refer to previous works [19][20][21][22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Twelve quick steps for genome assembly and annotation in the classroom

et al. 2020

View full text Add to dashboard Cite

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

show abstract

Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

Cited by 14 publications

References 12 publications

Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

African Arowana Genome Provides Insights on Ancient Teleost Evolution

Twelve quick steps for genome assembly and annotation in the classroom

Contact Info

Product

Resources

About