Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.

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Ma, K. Y., Chan, T. ‐Y & Chu, K. H. (2011). Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. —Zoologica Scripta, 40, 498–508. The taxonomic revision in 1997 of the shrimps formerly classified in Penaeus s.l. has been one of the most controversial issues on systematics of the decapods in recent years. Since Pérez Farfante & Kensley (Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) split this long‐accepted taxon into six genera, much debate has been devoted to their proposed new classification scheme; this has taken place because there are serious doubts whether the said scheme could reflect the evolutionary relationships among the 29 Penaeus s.l. species. Although these shrimps can be easily separated into several groups morphologically, whether these subdivisions are truly monophyletic and warrant a generic rank continues to be hotly debated among taxonomists. This study examined a total of 2425 bp sequences from three nuclear protein genes (enolase, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α‐subunit), and the mitochondrial 16S and 12S rRNA gene of 18 Penaeus s.l. shrimps and 13 other species in the family Penaeidae. Our phylogenetic analyses strongly support the monophyly of Penaeus s.l. and, concurring with previous studies that used the mitochondrial genes alone, the paraphyly of both Penaeus s.s. (sensu Pérez Farfante & Kensley, Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) and Melicertus, rendering them non‐natural groupings. Our study reveals two lineages: Penaeus s.s. + Fenneropenaeus + Litopenaeus + Farfantepenaeus and Melicertus + Marsupenaeus, which exhibit genetic divergences comparable with those among other penaeid genera. However, all the morphological characters, which are emphasized by Pérez Farfante and Kensley and used to separate Penaeus s.l., do not correlate with the grouping revealed by the present, perhaps decisive, phylogenetic result. Such disparity may arise from selection on the morphology of genitalia and convergent evolution. Our molecular data clearly refute the six‐genus classification, and we advocate the restoration of the old Penaeus genus (=Penaeus s.l.) definition which is the only classification scheme with both the morphological and the molecular data being in agreement.

Two acorn barnacles, Tetraclita japonica japonica and Tetraclita japonica formosana, have been recently reclassified as two subspecies, because they are morphologically similar and genetically indistinguishable in mitochondrial DNA sequences. The two barnacles are distinguishable by parietes colour and exhibit parapatric distributions, coexisting in Japan, where T. j. formosana is very low in abundance. Here we investigated the genetic differentiation between the subspecies using 209 polymorphic amplified fragment length polymorphism markers and 341 individuals from 12 locations. The subspecies are genetically highly differentiated (phi(CT) = 0.267). Bayesian analysis and principal component analysis indicate the presence of hybrids in T. j.formosana samples from Japan. Strong differentiation between the northern and southern populations of T. j. japonica was revealed, and a break between Taiwan and Okinawa was also found in T. j. formosana. The differentiation between the two taxa at individual loci does not deviate from neutral expectation, suggesting that the oceanographic pattern which restricts larval dispersal is a more important factor than divergent selection in maintaining genetic and phenotypic differentiation. The T. j. formosana in Japan are probably recent migrants from Okinawa, and their presence in Japan may represent a poleward range shift driven by global warming. This promotes hybridization and might lead to a breakdown of the boundary between the subspecies. However, both local adaptation and larval dispersal are crucial in determining the population structure within each subspecies. Our study provides new insights into the interplay of local adaptation and dispersal in determining the distribution and genetic structure of intertidal biota and the biogeography of the northwestern Pacific.

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

Abstract. The kuruma shrimp Penaeus japonicus Bate, 1888 (Decapoda : Penaeidae) is economically important in the global shrimp market. It was regarded as the only species in the subgenus Marsupenaeus. However, our previous molecular analyses revealed two cryptic species (Forms I and II) in this species complex. In this study, we confirm the phylogenetic relatedness between the two cryptic species; revise their taxonomic status; and review their range distribution. The name Penaeus pulchricaudatus Stebbing, 1914 (with type-locality off the eastern coast of South Africa), previously considered as a junior synonym of P. japonicus, is fixed for Form II through a neotype selection. P. japonicus (Form I) is only confined to the East China Sea (including Japan, its type-locality) and the northern South China Sea. P. pulchricaudatus is widely distributed in the South China Sea, Australia, the Red Sea, the Mediterranean, and the western Indian Ocean. Phylogenetic analysis shows that P. japonicus is genetically homogeneous yet P. pulchricaudatus exhibits a strong phylogeographical structure. The Mediterranean stock of P. pulchricaudatus originated from the Red Sea population, supporting the Lessepsian migration hypothesis. The presence of two closely related cryptic species in the P. japonicus species complex provides important insights into fishery management and aquaculture development.

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