Dataset Information

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense.

ABSTRACT:

Background

The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement.

Results

We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ?4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes.

Conclusion

The first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.

SUBMITTER: Jin S

PROVIDER: S-EPMC7812440 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense.

Jin Shubo S Bian Chao C Jiang Sufei S Han Kai K Xiong Yiwei Y Zhang Wenyi W Shi Chengcheng C Qiao Hui H Gao Zijian Z Li Ruihan R Huang Yu Y Gong Yongsheng Y You Xinxin X Fan Guangyi G Shi Qiong Q Fu Hongtuo H

GigaScience 20210101 1

<h4>Background</h4>The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement.<h4>Results</h4>We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-gen ...[more]

PMID: 33459341

Similar Datasets

Project description:BackgroundThe oriental river prawn (Macrobrachium nipponense) is the most prevalent aquaculture species in China. The sexual precocity in this species has received considerable attention in recent years because more and more individuals matured at a small size, which devalues the commercial production. In this study, we developed deep-coverage transcriptomic sequencing data for the ovaries of sexually precocious and normal sexually mature M. nipponense using next-generation RNA sequencing technology and attempted to provide the first insight into the molecular regulatory mechanism of sexual precocity in this species.ResultsA total of 63,336 unigenes were produced from the ovarian cDNA libraries of sexually precocious and normal sexually mature M. nipponense using Illumina HiSeq 2500 platform. Through BLASTX searches against the NR, STRING, Pfam, Swissprot and KEGG databases, 15,134 unigenes were annotated, accounting for 23.89% of the total unigenes. 5,195 and 3,227 matched unigenes were categorized by GO and COG analysis respectively. 15,908 unigenes were consequently mapped into 332 KEGG pathways, and many reproduction-related pathways and genes were identified. Moreover, 26,008 SSRs were identified from 18,133 unigenes. 80,529 and 80,516 SNPs were yielded from ovarian libraries of sexually precocious and normal sexually mature prawn, respectively, and 29,851 potential SNPs between these two groups were also predicted. After comparing the ovarian libraries of sexually precocious and normal sexually mature prawn, 549 differentially expressed genes (DEGs) and 9 key DEGs that may be related to sexual precocity of M. nipponense were identified. 20 DEGs were selected for validation by quantitative real-time PCR (QPCR) and 19 DEGs show consistent expression between QPCR and RNAseq-based differential expression analysis datasets.ConclusionThis is the first report on the large-scale RNA sequencing of ovaries of sexually precocious and normal sexually mature M. nipponense. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of M. nipponense. The large number of candidate SNPs and SSRs detected in this study could be used as genetic markers for population genetics and functional genomics in this species. More importantly, many DEGs, especially nine key DEGs between sexually precocious and normal sexually mature prawns were identified, which will dramatically improve understanding of molecular regulatory mechanism of sexual precocity of this species.

Dataset Information

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense.

Background

Results

Conclusion

Publications

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets