Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

Emerging research organisms enable the study of biology that cannot be addressed using classical “model” organisms. The development of novel data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.Primary Findings-Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis-Combined short- and long-read RNA-Seq improves the Parhyale genome annotation-ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements-NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding-Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics-Integration of accessibility and gene expression reveals possible enhancers and repressors-Omni-ATAC can identify known and novel regulatory elements

Phylogenetic analysis of TALE superclass homeobox genes in amphipod crustaceans

TALE class genes are a group of developmentally conserved transcription factors found in animals. Here, we describe the identification and phylogenetic analysis of TALE class genes in amphipod crustaceans. We identified 241 putative TALE class genes from 56 amphipod crustacean species. Phylogenetic analysis of the genes revealed six subclasses. We provide a list of FASTA sequences of the genes identified. Results from this work may inform future evolutionary and comparative genomics studies on animal development.

First Report of Cyamus Boopis from A Humpback Whale (Megaptera novaeangliae) in the Coastal East China Sea

Background: Cyamus boopis is an amphipod crustacean that obligately parasitizes the body surface of the humpback whale, Megaptera novaeangliae. The life cycle of C. boopis does not include a swimming stage, and the crustacean spends its entire life on the body of M. novaeangliae. Methods: On November 15, 2017, a male humpback whale was found stranded on the coast of the cape of Yuan Tuo, Qidong, Nantong, JiangSu province, China. Parasites were collected from the carcass of this whale and identified by morphological techniques and molecular analysis. Results: A total of 15 C. boopis specimens were collected, and eight females and seven males were morphologically identified. A phylogenetic tree of cytochrome c oxidase subunit 1 revealed that the collected specimens clustered together with previously reported C. boopis sequences from the Northern Hemisphere. Conclusion: This is the first report of C. boopis in a humpback whale from the East China Sea and supplements data from humpback whales found off the coast of China. In addition, our data provide supplementary data on the migration paths of humpback whales.

PARAMETERS OF THE FECUNDITY OF AMPHIPOD CRUSTACEAN ALIEN SPECIES (CRUSTACEA, AMPHIPODA) FROM WATERCOURSES OF BELARUS

For the first time for water bodies of Belarus, based on studies (2008–2015), the main fertility parameters for eight alien species of amphipods were established . The minimum sizes of individuals for which identification of sex and the size of sexual maturation is possible are presented. The ranges of the body length of the egg-bearing females and the average sizes of the breeding individuals were determinate. The sizes and number of eggs are given at three stages of development for females of different age groups. Absolute and relative fertility were revealed. It is established that the number of eggs in the brood bag correlates with the size and weight of the female; the dependences of fecundity on the length and weight of the female were calculated. The theoretical possible number of litters in the period of reproduction of animals in the conditions of the obtained range was determined. The obtained results differed insignificantly with the literature data from regions with similar climatic conditions, that was determined mainly by various ecological conditions.

Shape and size of the arenas affect amphipod behaviours: implications for ecotoxicology

The use of behaviour in ecotoxicology is expanding, however the lack of standardisation and validation of these assays currently presents a major drawback in moving forward in the development of behavioural assays. Furthermore, there is a current paucity of control data on test species, particularly invertebrate models. In this study we assessed a range of behaviours associated with spatial distribution and locomotion in relation to arena size and shape in two species of amphipod crustacean (Echinogammarus marinus and Gammarus pulex). Arena shape had significant effects on almost all behavioural parameters analysed. Increasing arena size resulted in an increased mean velocity and activity plus increased proportional use of the central zones. These results indicate that ‘ceiling effects’ may occur in some ecotoxicological studies resulting in potentially ‘false’ negative effects if careful consideration is not paid to experimental design. Differences in behaviours were observed between the two species of amphipod. For example, G. pulex spend approximately five times (∼20%) more of the available time crossing the central zones of the arenas compared to E. marinus (∼4%) which could have implications on assessing anxiolytic behaviours. The results of this study highlight several behaviours with potential for use in behavioural ecotoxicology with crustaceans but also underscore the need for careful consideration when designing these behavioural assays.