First Insights into the Subterranean Crustacean Bathynellacea Transcriptome: Transcriptionally Reduced Opsin Repertoire and Evidence of Conserved Homeostasis Regulatory Mechanisms

<div><p>Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of <i>Allobathynella bangokensis</i> using RNA-seq. <i>De novo</i> sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea <i>Daphnia pulex</i>. In the <i>A</i>. <i>bangokensis</i> transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i.e. arthropsins, peropsins, and melaopsins), suggesting potential regressive adaptation to the dark environment. However, <i>A</i>. <i>bangokensis</i> expressed conserved gene family sets, such as heat shock proteins and those related to key innate immunity pathways and antioxidant defense systems, at the transcriptional level, suggesting that this species has evolved adaptations involving molecular mechanisms of homeostasis. The transcriptomic information of <i>A</i>. <i>bangokensis</i> will be useful for investigating molecular adaptations and response mechanisms to subterranean environmental conditions.</p></div

Summary of the statistics from the transcriptomic analysis of the subterranean crustacean <i>Allobathynella bangokensis</i>.

<p>Summary of the statistics from the transcriptomic analysis of the subterranean crustacean <i>Allobathynella bangokensis</i>.</p

List of eye-related genes identified in the <i>Allobathynella bangokensis</i> transcriptome, presented with RPKM values and matching species information.

<p>The genes and reference protein IDs of <i>Daphnia pulex</i> were adopted from a previous study [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170424#pone.0170424.ref037" target="_blank">37</a>].</p

Analysis of heat shock protein superfamily of the <i>Allobathynella bangokensis</i>.

<p>The compositions and percentage rankings of the <i>Allobathynella bangokensis</i> heat shock protein (<i>Hsp</i>) superfamily (A) and their basal transcript levels represented by RPKM values (B). Detailed information is appended in the supplementary materials (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170424#pone.0170424.s011" target="_blank">S8 Table</a>).</p

Toll-like receptor and JAK-STAT signaling pathway.

<p><i>Allobathynella bangokensis</i> transcripts coding for the corresponding enzymes of the A) Toll-like receptor and B) JAK-STAT signaling pathways from the KEGG database. The annotated enzymes are shown in pink boxes.</p

The composition of Malacostraca KEGG analysis.

<p>The compositions and percentage rankings of the A) <i>Allobathynella bangokensis</i>, B) amphipod <i>Hyalella azteca</i>, C) amphipod <i>Melita plumulosa</i>, and D) isopod <i>Asellus aquaticus</i> KEGG pathways. Detailed information is appended in the supplementary materials (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170424#pone.0170424.s009" target="_blank">S6 Table</a>).</p

The most abundant InterPro domain classifications of <i>Allobathynella bangokensis</i> transcript contigs.

<p>The most abundant InterPro domain classifications of <i>Allobathynella bangokensis</i> transcript contigs.</p

BLAST top hit species distribution.

<p>Number of top BLAST hit species identified for the <i>Allobathynella bangokensis</i> transcript contigs (A) and pie charts presenting the annotated genes and their corresponding phylum (B) and class (C). Detailed information is appended in the supplementary materials (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170424#pone.0170424.s005" target="_blank">S2 Table</a>).</p

Antioxidant defense system in <i>Allobathynella bangokensis</i>.

<p>A) Schematic diagram representing a proposed cascade for the antioxidant defense system, along with RPKM values of the <i>Allobathynella bangokensis</i> transcripts coding for the corresponding enzymes in this system. B) Phylogenetic tree of glutathione <i>S</i>-transferase (GST) proteins from <i>A</i>. <i>bangokensis</i> and from arthropods constructed by the Bayesian method.</p