The Complete Mitochondrial Genome of Entemnotrochus rumphii, a Living Fossil for Vetigastropoda (Mollusca: Gastropoda)

Incorporation of microgastropoda species provides novel insights into phylogeny of Trochoidea (Gastropoda: Vetigastropoda)

Trochoidea is the richest and most diverse group within Vetigastropoda, serving as one of the main focuses on studies of marine ecology and systematics. Both morphological and molecular studies have sought to resolve the phylogenetic framework of Trochoidea; however, the phylogenetic relationships among some lineages remain controversial. In order to explore the phylogenetic relationships within Trochoidea, we sequenced the mitochondrial genomes of 9 trochoids and analyzed them with data from 38 previously published mitochondrial genomes and 27 transcriptomic data representing 11 families within this group. The mitochondrial genomes of all Trochidae exhibited a consistent gene arrangement and showed conserved genome size and nucleotide composition; however, Colloniidae and Phasianellidae showed higher levels of gene order rearrangement. Furthermore, three-nucleotide insertions were observed in the cox1 gene of Colloniidae and nad4L gene of Phasianellidae, while three-nucleotide deletions were detected in nad4 gene of Trochidae. Both maximum likelihood and Bayesian inference analyses supported the monophyly of all families within the Trochoidea, except Tegulidae, and placed Liotiidae as sister to the rest of Trochoidea with poor to moderate support. Areneidae was recovered as the sister group to a clade including Phasianellidae and Colloniidae. These findings challenge the traditional classification of this family based on both morphological and molecular data. Our study provides new insights into the phylogeny of Trochoidea, especially with the incorporation of micromolluscs taxa, and highlight the significance of incorporating microgastropoda taxa into molecular phylogenetic reconstructions of gastropod subgroups.

Complementing aculiferan mitogenomics: comparative characterization of mitochondrial genomes of Solenogastres (Mollusca, Aplacophora)

BACKGROUND

With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class of aplacophoran molluscs - Solenogastres (or Neomeniomorpha) - is still neglected.

RESULTS

Here, we present six new mitochondrial genomes from five families of Solenogastres (Amphimeniidae, Gymnomeniidae, Proneomeniidae, Pruvotinidae, Simrothiellidae), including the first complete mitogenomes, thereby now representing three of the four traditional orders. Solenogaster mitogenomes are variable in size (ranging from approximately 15,000 bp to over 17,000 bp). The gene order of the 13 protein coding genes and two rRNA genes is conserved in three blocks, but considerable variation occurs in the order of the 22 tRNA genes. Based on phylogenetic analyses and reconstruction of ancestral mitochondrial genomes of Aculifera, the position of (1) trnD gene between atp8 and atp6, (2) trnT and P genes between atp6 and nad5, and (3) trnL1 gene between G and E, resulting in a 'MCYWQGL1E'-block of tRNA genes, are all three considered synapomorphies for Solenogastres. The tRNA gene block 'KARNI' present in Polyplacophora and several conchiferan taxa is dissolved in Solenogastres.

CONCLUSION

Our study shows that mitogenomes are suitable to resolve the phylogenetic relationships among Aculifera and within Solenogastres, thus presenting a cost and time efficient compromise to approach evolutionary history in these clades.

Transcriptome data for an ancient 'living-fossil' mollusc, Entemnotrochus rumphii

The Pleurotomarioidea, commonly referred to as slit shells, constitute one of the most ancient and enduring lineages within the phylum Mollusca, with its fossil record tracing back to the Upper Cambrian epoch. Its rareness and evolutionary antiquity surpass even that of the nautilus. In this study, we conducted the first transcriptome sequencing and analyses of Entemnotrochus rumphii (Schepman, 1879), a representative species of Pleurotomarioidea. Full-length transcriptome sequencing of E. rumphii was performed using the PacBio Sequel II platform with SMRT technology. A total of 64.38 gigabytes of data and 964,550 polymerase reads were generated, resulting in 28,068,998 subreads after data filtering. After de-duplication, correction, and clustering, we identified 19,273 genes. Additionally, next-generation sequencing was performed on 11 tissues of E. rumphii. This investigation provides a detailed portrayal and analytical scrutiny of its transcriptomic landscape.

Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae

BACKGROUND

The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes.

RESULTS

Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs.

CONCLUSION

The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei

The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.