De novo transcriptome reconstruction in aquacultured early life stages of the cephalopod Octopus vulgaris

Abstract

Cephalopods have been considered enigmatic animals that have attracted the attention of scientists from different areas of expertise. However, there are still many questions to elucidate the way of life of these invertebrates. The aim of this study is to construct a reference transcriptome in Octopus vulgaris early life stages to enrich existing databases and provide a new dataset that can be reused by other researchers in the field. For that, samples from different developmental stages were combined including embryos, newly-hatched paralarvae, and paralarvae of 10, 20 and 40 days post-hatching. Additionally, different dietary and rearing conditions and pathogenic infections were tested. At least three biological replicates were analysed per condition and submitted to RNA-seq analysis. All sequencing reads from experimental conditions were combined in a single dataset to generate a reference transcriptome assembly that was functionally annotated. The number of reads aligned to this reference was counted to estimate the transcript abundance in each sample. This dataset compiled a complete reference for future transcriptomic studies in O. vulgaris.

Identifying Natural Bioactive Peptides from the Common Octopus (Octopus vulgaris Cuvier, 1797) Skin Mucus By-Products Using Proteogenomic Analysis

“…In fact, the genome of O. vulgaris, although it is currently in progress, has not been completely sequenced and accurately annotated [ 19 ]. This is the reason why protein identification was conducted by using two databases: the Cephalopoda protein dataset from UniProtKB database, and the UniGene transcriptome database of O. vulgaris paralarvae [ 20 ]. However, despite using both databases, the results obtained showed 112 uncharacterized proteins while only 313 were recognized as proteins for the O. vulgaris species.…”

“…The mass spectra obtained in the LTQ-Orbitrap Elite instrument was compared and validated with a theoretical mass spectra by using the Cephalopoda protein dataset from the UniProtKB database (including canonical and isoforms sequences) containing 125,800 protein sequence entries and the UniGene transcriptome database of O. vulgaris paralarvae [ 20 ] containing 77,838 protein sequence entries. The software used for the analysis was SEQUEST-HT (Protein Discoverer 2.4, Thermo Fisher Scientific).…”

Transcriptome-wide selection and validation of a solid set of reference genes for gene expression studies in the cephalopod mollusk Octopus vulgaris

“…In cephalopods, the study of the molecular machinery occurring in these processes is still limited. Few studies of cuttlefish ( Agin et al, 2000 , 2001 , 2003 ; Focareta et al, 2014 ; Focareta and Cole, 2016 ; Bian et al, 2018 ), squid ( Giuditta et al, 2002 ; Kimbell and McFall-Ngai, 2003 ; Burbach et al, 2019 ), and octopus ( Zarrella, 2011 ; Zarrella et al, 2015 ; van Giesen et al, 2020 ; see also Prado-Álvarez et al, 2022 ) have been based on an exiguous number of specific candidate molecules involved in given functions or biological aspects of cephalopod plasticity.…”

Insights into Common Octopus (Octopus vulgaris) Ink Proteome and Bioactive Peptides Using Proteomic Approaches

“…In 1797, Cuvier first described O. vulgaris, which belongs to the family Octopodidae, as a benthic, neritic species that can be found in a variety of habitats, including rocks, coral reefs, and grass, from the shore to the outer edge of the continental shelf at depths ranging from 0 to 200 m [2]. Octopuses have the ability to learn, play and regenerate their damaged tissues, and they can also exhibit predatory and exploratory behavior [2,3]. In case of danger, they can squirt water at intruders to scare them away or cover themselves with ink for camouflage [4,5].…”

“…Depending on the life stage, paralarvae, and settlement stage, they inhabit two different habitats. During the paralarvae stage, which lasts from hatching to around 30-40 days, animals compose part of the zooplankton and gradually transition to a benthonic life in the settlement stage [3].…”