Elsevier

Marine Genomics

Volume 54, December 2020, 100783
Marine Genomics

De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus

https://doi.org/10.1016/j.margen.2020.100783Get rights and content

Abstract

The spiny lobster, Panulirus argus, is an ecologically relevant species in shallow water coral reefs and a target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster Panulirus argus assembled from short Illumina 150 bp PE raw reads. A total of 80,152,094 raw reads were assembled using the Oyster River Protocol pipeline. The assembly resulted in a total of 254,773 transcripts. Functional gene annotation was conducted using the software package ‘dammit’. Lastly, gene enrichment analyses were conducted using the Gene Ontology (GO) and KEGG pathway (Kaas) databases. This resource will be of utmost importance in future research aiming at exploring the effect of local and regional anthropogenic disturbances, as well as global climate change on the molecular physiology of this overexploited species.

Introduction

Within the order Decapoda, one of the most speciose crustacean clades (De Grave et al., 2009), clawless lobsters or clawless crayfish (infraorder Achelata), including spiny, coral, and slipper lobsters, differ markedly in their morphology, behavior, and ecology (De Grave et al., 2009; Lozano-Fernandez et al., 2019). In contrast to that reported for other decapod crustaceans, clawless lobsters lack chelae on the first pair of pereiopods and also share a unique larval type; the long-lived teleplanic phyllosomata (Kittaka and Abrunhosa, 1997). Representatives of the infraorder Achelata have captured the attention of evolutionary biologists during recent years; various species are currently used as model systems to understand the historical origin and adaptive value of most impressive traits (Patek and Oakley, 2003; Butler IV et al., 2015; Anderson et al., 2013; Baeza et al., 2016). Examples include, among others, the evolution of ‘behavioral immunity’ driven by viral pathogens (Butler IV et al., 2015), sound production that involves the use of an antennal stridulating organ to deter predators (Patek and Oakley, 2003), active parental care in concert with large reproductive expenditure at large body sizes (Baeza et al., 2016), and ontogenetic shifts in coloration, color pattern, and the static allometry of body parts driven by decreasing predation risk with increasing body size (Anderson et al., 2013). Genomic resources in the infraorder Achelata will help us continue improving our understanding of their remarkable evolutionary innovations (Kozma et al., 2018; Baeza, 2018; Baeza et al., 2019; Lozano-Fernandez et al., 2019).

The Caribbean spiny lobster, Panulirus argus (Latreille, 1804), is a keystone species in shallow water coral reefs (Higgs et al., 2016) and a target of the most lucrative fishery in the greater Caribbean region (Holthuis, 1981) (Fig. 1). Panulirus argus inhabits the western Atlantic from southern Brazil in the southern hemisphere to North Carolina in the northern hemisphere (Holthuis, 1981). The life history of P. argus is well known (Baeza et al., 2016; Baeza, 2018; Baeza et al., 2018 and references therein). Panulirus argus is fully exploited or overexploited across its entire geographic range (Holthuis, 1981). Despite the ecological relevance and commercial value of P. argus, few genomic resources exist for this species (Kozma et al., 2018; Baeza, 2018; Baeza et al., 2019). The development of such resources is relevant as it will help us to continue understanding the remarkable behavior and ecology of P. argus, while also aiding in improving fishery management and conservation strategies.

This study forms part of a comprehensive effort to develop genomic resources that are pivotal to improve our understanding of the biology of this remarkable species, as well as its management and conservation. Our aim was to assemble, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster Panulirus argus. For this purpose, we used the Oyster River Protocol for de novo transcriptome assembly (ORP). Overall, the ORP uses a standardized and benchmarked set of (multi-assembler and multi-kmer) bioinformatic processes that results in transcriptome assemblies with enhanced qualities over other standard assembly methods (MacManes, 2018).

Section snippets

Sampling of Panulirus argus

Field collection was approved by the FWCC (permit number: SAL-11-1319-SR). One adult female of P. argus (8.1 mm carapace length) was collected in July 2017 by hand from a patch reef on the ocean side of Long Key (N24°49′26″; W80°48′48″), Florida, USA and transported alive to Clemson University, Clemson, SC. In the laboratory, the specimen was maintained in a 500 l circular polyethylene container. The heart (+ hemolymph) was dissected and immediately snap-frozen within a 50 ml centrifuge tube

Conclusion

This study assembled for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster, P. argus, a keystone species in shallow water coral reefs and a target of the most lucrative fishery in the greater Caribbean region. This de novo assembled transcriptome will contribute to a better understanding of molecular responses to local, regional, and global anthropogenic disturbance in this overexploited species. Sequencing of the whole genome of P. argus is underway.

Data accesibility

Raw RNA-seq data has been deposited in the NCBI Sequence Read Archive (SRA) under project number PRJNA453553. The transcriptome annotated with the program dammit was deposited in Zenodo and is available (both fasta and gff3 files) at https://doi.org/10.5281/zenodo.3588230. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/ENA/GenBank under the accession GIHN00000000. The version described in this paper is the first version, GIHN01000000.

Author contributions

J. Antonio Baeza: Conceptualization, Methodology, Analysis (transcriptome annotation), Data curation, Writing, Original draft preparation. Visualization, Writing, Reviewing, and Editing. Matthew MacMannes: Conceptualization, Methodology, Analysis (transcriptome assembly and annotation), Data curation, Writing, Original draft preparation, Writing, Reviewing, and Editing.

Acknowledgements

JAB thanks Dr. Vincent P. Richards for bioinformatics support during the development of this project. Many thanks to Timothy Cronin for improving the English language of this manuscript. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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