Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles (Cirripedia: Balanomorpha)

The Mitochondrial Genome of the Globally Invasive Barnacle Megabalanus coccopoma Darwin 1854 (Crustacea: Balanomorpha): Rearrangement and Phylogenetic Consideration within Balanomorpha

Megabalanus coccopoma (Darwin, 1854) is a globally invasive species in Balanomorpha (Crustacea). This species is a model organism for studying marine pollution and ecology. However, its mitogenome remains unknown. The mitogenome sequencing of M. coccopoma is completed in the present study. It has a 15,098 bp in length, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), along with a putative regulatory area. A substantial A+T bias was observed in the genome composition (68.2%), along with a negative AT (0.82) and GC (−0.136) skew. Compared to the gene sequence of the ground model of pan-crustacea, 13 gene clusters (or genes), such as 10 tRNAs and 3 PCGs, were observed in a different order. This was in line with the previously observed large-scale gene rearrangements of Balanomorpha. Among the 37 genes, the gene cluster (M-nad2-W-cox1-L2-cox2-D-atp8-atp6-cox3-G- nad3-R-N-A-E-S1) Balanomorpha was conserved. Furthermore, phylogeny analysis indicated that the existing Balanomorpha species family was divided into nine rearrangement patterns, supporting the polyphyly of Balanoidea.

The complete mitochondrial genome of Balanus trigonus (Thecostraca, Balanomorpha, Balanidae) from South Korea

The complete sequence of the mitochondrial genome of Balanus trigonus Darwin, 1854 was examined using next-generation sequencing analysis. The complete mitogenome of B. trigonus has 15,336 bp in length and comprises 37 genes, namely, 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. Both the gene order and characteristics are consistent with those of other species within the family Balanidae. Phylogenetic analysis based on complete mitogenomes revealed taxonomic relationships among members of the family Balanidae.

The first mitochondrial genome of Tetraclita kuroshioensis (Crustacea: Sessilia) from China: insight into the phylogeny within Cirripedia

We determined the first mitochondrial genome of Tetraclita kuroshioensis from China. The mitochondrial genome of T. kuroshioensis was found to be 15,175 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. The longest non-coding region was 425 bp in length. Phylogenetic analysis showed that T. kuroshioensis clustered with T. serrata and then clustered with T. squamosa squamosa with high bootstrap value (BP = 100). In the future, sequencing of additional mitochondrial genomes should provide additional insights into the deep phylogeny of Cirripedia.

The evolutionary diversity of barnacles, with an updated classification of fossil and living forms

We present a comprehensive revision and synthesis of the higher-level classification of the barnacles (Crustacea: Thecostraca) to the genus level and including both extant and fossils forms. We provide estimates of the number of species in each group. Our classification scheme has been updated based on insights from recent phylogenetic studies and attempts to adjust the higher-level classifications to represent evolutionary lineages better, while documenting the evolutionary diversity of the barnacles. Except where specifically noted, recognized taxa down to family are argued to be monophyletic from molecular analysis and/or morphological data. Our resulting classification divides the Thecostraca into the subclasses Facetotecta, Ascothoracida and Cirripedia. The whole class now contains 14 orders, 65 families and 367 genera. We estimate that barnacles consist of 2116 species. The taxonomy is accompanied by a discussion of major morphological events in barnacle evolution and justifications for the various rearrangements we propose.

The mitochondrial genome of Chthamalus malayensis (Sessilia: Chthamalidae) and its molecular phylogeny within Cirripedia

Cirripedia is a lower crustacean that has an invaluable place in several aspects of intertidal ecology and anti-fouling research. In this study, we present the first mitochondrial genome of Chthamalus malayensis. The complete mitochondrial genome of C. malayensis is a circular molecule of 15,230 bp. In comparison to the pancrustacean ground pattern, the mitochondrial genome of C. malayensis has a deletion of the trnC gene. Phylogenetic analysis based on mitochondrial protein-coding genes showed that C. malayensis clusters with C. antennatus (BP = 98) and is grouped with C. challengeri, Octomeris sp. BKKC-2014, and Notochthamalus scabrosus. Further studies are needed to reveal the specific phylogenic relationships within Cirripedia.

The first mitochondrial genome of Fistulobalanus albicostatus (Crustacea: Maxillopoda: Sessilia) and phylogenetic consideration within the superfamily Balanoidea

The first complete mitochondrial genome of the intertidal barnacle Fistulobalanus albicostatus Pilsbry, 1916 (Crustacea: Maxillopoda: Sessilia) is presented. The genome is a circular molecule of 15,665 bp, which encodes a set of 37 typical metazoan genes. All non-coding regions are 438 bp in length, with the longest one speculated as the control region (264 bp), which is located between srRNA and trnI. All protein-coding genes (PCGs) have an ATD (ATA, ATT, or ATG) start codon, except nad1, which is initiated with GTG. Remarkably, cox3, cob, nad1-5 have incomplete stop codons (T–– or TA–) and the remaining PCGs have the complete stop codon (TAA). Phylogenetic analysis based on 13 mitochondrial PCGs shows that the members of the Archaeobalanidae and Balanidae intermingle with species from Pyrgomatidae. The results supposed that Balanidae and Archaeobalanidae are non-monophyly.

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.

Mitochondrial genome of the acorn barnacle Tetraclita rufotincta Pilsbry, 1916: highly conserved gene order in Tetraclitidae

The complete mitochondrial genome of the intertidal barnacle Tetraclita rufotincta Pilsbry, 1916 (Crustacea: Maxillopoda: Sessilia) is presented. The genome is a circular molecule of 15,236 bp, which encodes a set of 37 typical metazoan mitochondrial genes. All non-coding regions are 438 bp in length, with the longest one speculated as the control region (242 bp), which is located between srRNA and trnK. Comparison of the genome and those of three other species from Tetraclitidae shows that gene arrangement is identical, indicating that the mitochondrial gene order is highly conserved in the family. Moreover, in comparison with the pancrustacean ground pattern, the four species of Tetraclitidae share three large conserved gene blocks. Phylogenetic analysis based on 13 mitochondrial PCGs shows that Chelonbia testudinaria (Coronulidae) clusters with the four species of Tetraclitidae. Within Tetraclitidae, T. serrata clusters with T. japonica, and the two grouped with T. rufotincta with high support (BP = 100), with T. divisa as the most distantly related species (BP = 100).