Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system

Cai, Mingyi; Zeng, Yu; Xiao, Shijun; Li, Wanbo; Han, Zhaofang; Han, Fang; Xiao, Junzhu; Liu, Fujiang; Wang, Zhiyong

doi:10.1038/s41597-019-0139-x

Cited by 30 publications

(27 citation statements)

References 39 publications

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“…The combination of nanopore long reads and the correction of Illumina short reads ensured the accuracy and completeness of genome assembly, and produced more ideal assembly indexes of contig N50 and less contig number than the genome assembly of several fish species using third-generation sequencing (Table S17) (Gong et al, 2018;Cai et al, 2019;Conte et al, 2019;Ge et al, 2019;He et al, 2019;Jiang et al, 2019; The O. macrolepis genome was annotated to produce 24,770 protein-coding genes (23,991 genes functionally annotated) and…”

Section: Discussionmentioning

confidence: 99%

“…Our results demonstrate the advantage of nanopore technology. The combination of nanopore long reads and the correction of Illumina short reads ensured the accuracy and completeness of genome assembly, and produced more ideal assembly indexes of contig N50 and less contig number than the genome assembly of several fish species using third‐generation sequencing (Table S17) (Gong et al., 2018; Cai et al., 2019; Conte et al., 2019; Ge et al., 2019; He et al., 2019; Jiang et al., 2019; Yang et al, 2019). Furthermore, physical mappings using Bionano and Hi‐C technology improved greatly the assembly of chromosome‐level genome.…”

Section: Discussionmentioning

confidence: 99%

“…High‐throughput chromatin conformation capture (Hi‐C) technology enables the generation of genome‐wide 3D proximity maps and is an efficient and low‐cost strategy for sequence clustering, ordering, and orientation for pseudomolecule construction (Burton et al., 2013). It has become a popular technology and has been successfully applied in many genome projects (Cai et al., 2019; Ge et al., 2019; He et al., 2019; Liu et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

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Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology

Sun

Gao

Wang

et al. 2020

Molecular Ecology Resources

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Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100‐fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi‐C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein‐coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non‐coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high‐quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology

Sun

Gao

Wang

et al. 2020

Molecular Ecology Resources

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“…All raw reads in FASTQ format were filtered using Trimmomatic software (version 0.36; [26]) based on the following criteria: (I) raw reads with sequencing adaptors; (II) a ratio of unidentified nucleotides in the raw reads ≥8%; and (III) raw reads that had more than 50% of base calls with a low quality score (Q<30). After filtering, we downloaded the whole-genome sequence of C. lucidus [27] and used it as a reference sequence for subsequent SNP filtering.…”

Section: Rad Data Processing and Snp Filteringmentioning

confidence: 99%

Population Genomics Provides Insights into the Population Structure and Climate-driven Adaptation of Collichthys Lucidus

Zhao

Song

et al. 2021

Preprint

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Background: Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the conservation and management of biological resources. Collichthys lucidus is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results: To elucidate the fine-scale genetic structure and local thermal adaptation of C. lucidus, we performed restriction site-associated DNA tag sequencing (RAD-seq) of 177 individuals from 8 populations, and a total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified. All the results revealed significant population structure with high support for two distinct genetic clusters, namely, the northern group (populations DL, TJ, LYG, NT, ZS, and WZ) and southern group (populations XM and ZH). The genetic diversity of the southern group was evidently lower than that of the northern group, which indicated that the southern group was possibly under climate-driven natural selection. In addition, a total of 314 SNPs were found to be significantly associated with temperature variation. Annotations of temperature-related SNPs suggested that genes involved in material (protein, lipid, and carbohydrate) metabolism and immune responses were critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. Conclusion: In the context of anthropogenic activities and environmental change, the results of the present population genomic work could make important contributions to the understanding of genetic differentiation and adaptation to changing environments.

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“…Current sequencing technologies and assembly algorithms change the genome sequencing landscape. Chromosomal assembly can be done through single-molecule sequencing and chromatin conformation capture (3C) data analysis [5][6][7] . PacBio and Illumina sequencing lay the fundamental layer of sequence scaffolds contiguity and resolve repetitive DNA regions 8,9 .…”

Section: Introductionmentioning

confidence: 99%

High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense

Utomo

Za²,

Aditama³

et al. 2019

Preprint

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Ganoderma boninense is the dominant fungal pathogen in causing Basal Stem Rot (BSR) disease on oil palm. The whole genome of this fungus was sequenced using PacBio RS II platforms to gain the whole-genome shotgun libraries. These libraries were smoothed with Illumina Hiseq 4000 paired end sequencing to polish the genome assembly. Subsequently, a combination of Dovetail Chicago and HiC libraries with the HiRise assembly pipeline revealed the 12 pseudo-chromosomes of G. boninense. This is the first report of chromosomal-scale genome assembly for the most important fungal pathogen on oil palm.

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Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system

Abstract: Collichthys lucidus ( C . lucidus ) is a commercially important marine fish species distributed in coastal regions of East Asia with the X 1 X 1 X 2 X 2 /X 1 X 2 Y multiple sex chromosome system. The karyotype for female C . lucidus is 2n = 48, while 2n = 47 for male ones. … Show more

Cited by 30 publications

References 39 publications

Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology

Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology

Population Genomics Provides Insights into the Population Structure and Climate-driven Adaptation of Collichthys Lucidus

High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense

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