First draft genome for the sand-hopper Trinorchestia longiramus

Abstract

Crustacean amphipods are important trophic links between primary producers and higher consumers. although most amphipods occur in or around aquatic environments, the family talitridae is the only family found in terrestrial and semi-terrestrial habitats. the sand-hopper Trinorchestia longiramus is a talitrid species often found in the sandy beaches of South Korea. In this study, we present the first draft genome assembly and annotation of this species. We generated ~380.3 Gb of sequencing data assembled in a 0.89 Gb draft genome. Annotation analysis estimated 26,080 protein-coding genes, with 89.9% genome completeness. Comparison with other amphipods showed that T. longiramus has 327 unique orthologous gene clusters, many of which are expanded gene families responsible for cellular transport of toxic substances, homeostatic processes, and ionic and osmotic stress tolerance. This first talitrid genome will be useful for further understanding the mechanisms of adaptation in terrestrial environments, the effects of heavy metal toxicity, as well as for studies of comparative genomic variation across amphipods. Background & SummaryAmphipoda is an order of malacostracan crustaceans, composed of more than 228 families with over 10,200 species 1 . Most members of Amphipoda are found in aquatic environments, with both freshwater and marine species that occur in diverse habitats 2-6 . However, only a few amphipods in the family Talitridae are found in terrestrial regions close to the water, and others are "semi-terrestrial, " with both littoral and terrestrial representatives 7 .Talitrids are one of the prevailing macrofaunal groups in coastal regions that live along the interface between the water and land. The coastal talitrids, also known as "sand-hoppers, " are considered key species for energy flow to higher trophic levels 8 . They play a crucial role in food web dynamics by feeding on algal-biomass 9 and detritus along sandy beaches. They then become the source of food for many invertebrates, fish, and birds 4,8 . Unfortunately, anthropogenic activity contributes to various types of pollutants in the coastal ecosystem, which impacts the survival of talitrids 10-12 and other macrofauna [13][14][15] . For this reason, many talitrids are used as model organisms for studies of metal toxicity 10-12 . In addition, previous work on talitrids examined levels of genetic variation 16,17 , behavioral adaptations 18 , osmoregulation 19 , and orientation studies 20 . Most of these studies were carried out along the North Sea and the Mediterranean Sea regions.Despite such biological and ecological significance, no genome studies have been performed on any talitrid species, and only three genomes have been studied among the entire amphipod order. These included (1) Eulimnogammarus verrucosus (Family: Eulimnogammaridae) 21 , a freshwater amphipod from Baikal Lake; (2) Hyalella azteca (Family: Hyalellidae) 22 , another freshwater amphipod that lives by burrowing in the sediments; and (3) Parhyale hawaiensis (Family: Hyalidae) 23 . Tr...

The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods

“…4J-4K and 4Q-4R). To our surprise, the best blast hits for obtained sequences were unknown proteins from other crustacean species (Table S4) Patra et al, 2020). It is important to note that different proteins of the pheromone/odorant-binding family bind a wide range of hydrophobic molecules and function beyond chemoreception (Pelosi et al, 2018).…”

The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis

“…Currently, there are only two complete mitochondrial genome sequences of Platorchestia: P. parapacifica and P. japonica (Yang et al, 2017 ). Among 228 families consisting of more than 10,200 species in the order Amphipoda, only four genomes have been studied (Zeng et al, 2011 ; Rivarola-Duarte et al, 2014 ; Poynton et al, 2018 ; Patra et al, 2020 ), which includes the genome of talitrid Trinorchestia longiramus (Patra et al, 2020 ). Thus, we sequenced and assembled a reference genome for this Platorchestia species with an aim to set up a genetic platform for studying their taxonomical identification, divergence, and evolutionary history.…”

“…A phylogenetic analysis with 13 arthropod species suggested that P. hallaensis diverged from T . longiramus (Patra et al, 2020 ) during the Middle Cenozoic era. This talitrid genome will play a key role in further studies on the molecular mechanisms for adaptation of talitrids in diverse habitats and genomic variation across amphipods.…”

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“…Currently, there are only two complete mitochondrial genome sequences of Platorchestia: P. parapacifica and P. japonica (Yang et al, 2017). Among 228 families consisting of more than 10,200 species in the order Amphipoda, only four genomes have been studied (Zeng et al, 2011;Rivarola-Duarte et al, 2014;Poynton et al, 2018;Patra et al, 2020), which includes the genome of talitrid Trinorchestia longiramus (Patra et al, 2020). Thus, we sequenced and assembled a reference genome for this Platorchestia species with an aim to set up a genetic platform for studying their taxonomical identification, divergence, and evolutionary history.…”

“…The comparative genomics among 13 arthropod species identified unique gene clusters in P. hallaensis, as well as contracted and expanded gene clusters in 13 arthropod species and their ancestors. A phylogenetic analysis with 13 arthropod species suggested that P. hallaensis diverged from T. longiramus (Patra et al, 2020) during the Middle Cenozoic era. This talitrid genome will play a key role in further studies on the molecular mechanisms for adaptation of talitrids in diverse habitats and genomic variation across amphipods.…”