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A chromosome-level assembly of the black tiger shrimp ( Penaeus monodon ) genome facilitates the identification of novel growth-associated genes
- Publication Year :
- 2020
- Publisher :
- HAL CCSD, 2020.
-
Abstract
- The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.
- Subjects :
- growth-associated
[SDV]Life Sciences [q-bio]
Sequence assembly
Computational biology
Genome
Penaeus monodon
03 medical and health sciences
transcriptomics
Hi-C
14. Life underwater
Black tiger shrimp
genes
Genome size
reference genome
030304 developmental biology
2. Zero hunger
Comparative genomics
Whole genome sequencing
PacBio
0303 health sciences
biology
[SDV.BA]Life Sciences [q-bio]/Animal biology
04 agricultural and veterinary sciences
Genome project
biology.organism_classification
040102 fisheries
0401 agriculture, forestry, and fisheries
Reference genome
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....956f80caf81035e9a5e197fb3b5b110c