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.

Keywords: Candidate sex-related genes; Chromosome-level genome; Evolutionary analysis; Genome duplication; Macrobrachium nipponense.

Figure 1:

Picture of the sequenced oriental river prawn. This individual was collected from Taihu Lake, Wuxi City, Jiangsu Province, China.

Figure 2:

Hi-C interaction heat map and Circos view for the oriental river prawn genome. (A) A total of 49 chromosomes were constructed by Hi-C sequencing. (B) Circos view of the oriental river prawn. Layers include (1) chromosome length (Mb) and numbers; (2) distribution of gene density in 1-Mb non-overlapping windows; (3) distribution of repeat density in 1-Mb non-overlapping windows, with deeper green color indicating higher repeat density; and (4) distribution of GC content in 1-Mb non-overlapping windows, with pink lines representing inner synteny blocks.

Figure 3:

The divergence tree and the 4dTv results. (A) The divergence tree of 7 representative species. The numbers in parentheses represent confidence intervals. (B) The 4dTv distributions of oriental river prawn vs oriental river prawn (red) and oriental river prawn vs penaeid shrimp (blue).

Figure 4:

Sex-related candidate genes in the assembled oriental river prawn genome.