Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

Abstract

The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

COI gene sequencing reveals genetic population structuring and a separate lineage of the green tiger prawn Penaeus semisulcatus in the Gulf of Suez and the Bitter Lakes, Egypt

“…to a genetic transcriptional level. For instance, the P. pulchricaudatus exhibits higher background expression of heat shock proteins, which can be an indicator for superior thermal tolerance of P. pulchricaudatus over P. japonicus (Wang et al, 2020). Hence, it appears essential to provide more contribution for the taxonomy of different penaeids.…”

“…The family Penaeidae (first described by Rafinesque in 1815) comprises 226 species in 32 genera, 77% of which are located in the Indo-Pacific (Ditty, 2014). This is possibly related to the central Indo-Western Pacific origin of genus Penaeus, which passed through several eastward and westward migrations, founder effects, and speciation events, especially as a result of Pleistocene glaciations (Alam et al, 2017;Wang et al, 2020).…”

Muscle Transcriptome Analysis Reveals Molecular Mechanisms of Superior Growth Performance in Kuruma Shrimp, Marsupenaeus japonicus

“…Marsupenaeus japonicus, also known as kuruma shrimp and Japanese tiger prawn, is widely distributed in the Indo-West Pacific waters, eastern Africa, the Red Sea, and the Mediterranean Sea [1]. In China, it is mainly found in the waters south of the mouth of the Yangtze River [2,3]. M. japonicus is one of the most important farmed shrimp species in the world.…”

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomics Analysis Provides a New Perspective Into Unsynchronized Growth in Kuruma Shrimp (Marsupenaeus japonicus)

“…Kuruma shrimp Marsupenaeus japonicus is a broadly farmed economical shrimp species in the Indo-West Pacific region in both tropical and subtropical waters (Wang et al, 2018(Wang et al, , 2020Liu et al, 2019), where the supply of wild M. japonicus cannot meet the demand. So, shrimp farming industry developed fast in recent years to fill the gap (Jung et al, 2013).…”