Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species.

Jianbo Yuan,Xiaojun Zhang,Fuhua Li,Jianhai Xiang

doi:10.3389/fgene.2021.658619

Abstract

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.

Highlights

Penaeid shrimp belongs to Penaeidae, a family of Decapoda (Crustacea), which comprise many aquatic animals with high ecological and economic values, such as the Pacific white shrimp Litopenaeus vannamei, Chinese shrimp Fenneropenaeus chinensis, giant tiger prawn Penaeus monodon, and kuruma prawn Marsupenaeus japonicus (Farfante and Kensley, 1997; Wilson et al, 2000; Koyama et al, 2010)
A K-merbased genome survey was performed on the Illumina sequencing data of four representative penaeid shrimp species, L. vannamei, F. chinensis, P. monodon, and M. japonicus
The genome size estimated based on the K-mer depth of Peak B was half of that based on Peak A and half of that estimated by flow cytometry methods (Alcivar-Warren et al, 1997; Zhang et al, 2019)

Summary

Introduction

Penaeid shrimp belongs to Penaeidae, a family of Decapoda (Crustacea), which comprise many aquatic animals with high ecological and economic values, such as the Pacific white shrimp Litopenaeus vannamei, Chinese shrimp Fenneropenaeus chinensis, giant tiger prawn Penaeus monodon, and kuruma prawn Marsupenaeus japonicus (Farfante and Kensley, 1997; Wilson et al, 2000; Koyama et al, 2010). These species are the subject of the most important group in fisheries and aquaculture and have attracted considerable research attention (Dall et al, 1990). Due to their high commercial values, genome-based selective breeding programs have been conducted to ensure sustainable and profitable production

Methods

Results

Conclusion