Octocoral mitochondrial genomes provide insights into the phylogenetic history of gene order rearrangements, order reversals, and cnidarian phylogenetics

New mitochondrial gene order arrangements and evolutionary implications in the class Octocorallia

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date, seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole class Octocorallia, have been often overlooked. Here, we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from 7 to 14 and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT and GC skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, inverted transpositions and transpositions. Furthermore, gene order rearrangement events were restricted only to some regions of the tree. Overall, different rearrangement events arose independently and from the ancestral and most common gene order, instead of being derived from other rearranged orders. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.

The complete mitochondrial genome of the bubble-gum coral Paragorgia papillata (Octocorallia: Coralliidae) from the seamount in the tropical Western Pacific

The complete mitochondrial genome of Paragorgia papillata Li et al. 2021, a deep-sea gorgonian inhabiting at 858 m in Caroline Ridge, was obtained in this study. The length of the mitochondrial genome is 19,018 bp with 14 protein coding genes, one transfer RNA (tRNA-Met) and two ribosomal RNA genes contained in this circular molecule. Phylogenetic analysis indicated that P. papillata and P. coralloides Bayer, 1993 were two closely related species, and a total of 26 mutational sites (four nonsynonymous mutations included) can be detected between their mitochondrial genomes. This exhibits a case that mitochondrial genomes can be applied to differentiate closely related species in gorgonians. The phylogenetic tree constructed with mitochondrial genomes showed that the families in Octocorallia are reciprocally monophyletic, provided that the family names were revised according to the systematic revision of Octocorallia guided by phylogenomics. However, the relationships of the families within each order were different between the previous phylogenomic work and ours. Integrating mitochondrial genomes from a wider array of Octocorallia families is essential for a more accurate comparison of phylogenies derived from nuclear and mitochondrial sequences in future study.

The Mitogenome of the Subarctic Octocoral Alcyonium digitatum Reveals a Putative tRNAPro Gene Nested within MutS

We sequenced and analyzed the complete mitogenome of a Norwegian isolate of the octocoral Alcyonium digitatum using the Ion Torrent sequencing technology. The 18,790 bp circular mitochondrial genome was found to harbor the same set of 17 genes, which encode 14 protein subunits, two structural ribosomal RNAs and one tRNA, as reported in other octocorals. In addition, we detected a new tRNAPro-like gene sequence nested within the MutS protein coding region. This putative tRNA gene feature appears to be conserved among the octocorals but has not been reported previously. The A. digitatum mitogenome was also shown to harbor an optional gene (ORFA) that encodes a putative protein of 191 amino acids with unknown function. A mitogenome-based phylogenetic analysis, presented as a maximum likelihood tree, showed that A. digitatum clustered with high statistical confidence with two other Alcyonium species endemic to the Mediterranean Sea and the Southeast Pacific Ocean.

Skimming genomes for systematics and DNA barcodes of corals

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes

Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.

Complete mitochondrial genome of the abyssal coral Abyssoprimnoagemina Cairns, 2015 (Octocorallia, Primnoidae) from the Clarion-Clipperton Zone, Pacific Ocean

The Clarion-Clipperton Zone (CCZ) in the tropical East Pacific is a region of interest for deep-sea mining due to its underwater deposits of polymetallic nodules containing economically important metals such as nickel, copper, and cobalt. It is also a region of extensive baseline studies aiming to describe the state of the environment, including the biodiversity of the benthic fauna. An abundant component of the abyssal plain ecosystem consists of sessile fauna which encrusts polymetallic nodules and are vulnerable to potential impacts arising from exploitation activities, particularly removal of substrate. Therefore, this fauna is often considered to have key species whose genetic connectivity should be studied to assess their ecological resilience. One such species is Abyssoprimnoagemina Cairns, 2015, a deep-sea coral from the CCZ whose presence in the Interoceanmetal Joint Organization (IOM) claim area has been confirmed during samplings. In this study, we used next-generation sequencing (NGS) to obtain the 18S nuclear rRNA gene and the complete mitochondrial genome of A.gemina from IOM exploration area. The mitogenome is 18,825 bp long and encodes for 14 protein coding genes, 2 rRNAs, and a single tRNA. The two phylogeny reconstructions derived from these data confirm previous studies and display A.gemina within a highly supported cluster of seven species whose mitogenomes are all colinear and of comparable size. This study also demonstrates the suitability of NGS for DNA barcoding of the benthic megafauna of the CCZ, which could become part of the IOM protocol for the assessment of population diversity and genetic connectivity in its claim area.

The complete mitochondrial genome of soft coral, Eleutherobia rubra (Brundin, 1896) (Cnidaria; Anthozoa; Malacalcyonacea; Alcyoniidae)

The mitogenome of a soft coral, Eleutherobia rubra (Brundin, 1896), was completely sequenced for the first time. The total mitogenome length of E. rubra is 18,724 bp with 14 protein-coding genes, two ribosomal RNA genes, one transfer RNA gene (tRNA-Met), and one non-coding region (NCR). The gene order is also consistent with other Alcyoniidae species. The base composition is 30.1% A, 16.7% C, 19.5% G, and 33.7% T, with a G-C content of 36.2%. This is the first record of the complete mitogenome sequence of the genus Eleutherobia.

New Record of Dendronephthya sp. (Family: Nephtheidae) from Mediterranean Israel: Evidence for Tropicalization?

Bio-invasions have the potential to provoke cascade effects that can disrupt natural ecosystems and cause ecological regime shifts. The Mediterranean Sea is particularly prone to bio-invasions as the changing water conditions, evoked by climate change, are creating advantageous conditions for Lessepsian migrants from the Red Sea. Recently, in May 2023, a new alien species was documented in the Mediterranean Sea-a soft coral of the genus Dendronephthya. This discovery was made by divers conducting 'Long-Term Ecological Research' surveys, along the coast of Israel, at a depth of 42 m. Genetic and morphological testing suggest that the species identity may be Dendronepthya hemprichi, an Indo-Pacific coral, common in the Red Sea. According to life history traits of this species, such as accelerated attachment to available surfaces and fast growth, we expect it to rapidly expand its distribution and abundance across the Mediterranean Sea.

Mitochondrial genome comparison reveals the evolution of cnidarians

Cnidarians are the most primitive metazoans, but their evolutionary relationships are poorly understood, although recent studies present several phylogenetic hypotheses. Here, we collected 266 complete cnidarian mitochondrial genomes and re-evaluated the phylogenetic relationships between the major lineages. We described the gene rearrangement patterns of Cnidaria. Anthozoans had significantly greater mitochondrial genome size and lower A + T content than medusozoans. Most of the protein-coding genes in anthozoans such as COX 13, ATP6, and CYTB displayed a faster rate of evolution based on selection analysis. There were 19 distinct patterns of mitochondrial gene order, including 16 unique gene orders in anthozoans and 3 mtDNA gene orders pattern in medusozoans, were identified among cnidarians. The gene order arrangement suggested that a linearized mtDNA structure may be more conducive to Medusozoan mtDNA stability. Based on phylogenetic analyses, the monophyly of the Anthozoa was strongly supported compared to previous mitochondrial genome-based analyses rather than octocorals forming a sister group relationship with medusozoans. In addition, Staurozoa were more closely related to Anthozoa than to Medusozoa. In conclusion, these results largely support the traditional phylogenetic view of the relationships of cnidarians and provide new insights into the evolutionary processes for studying the most ancient animal radiations.

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.

Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes

In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.

Evolution of mitochondrial and nuclear genomes in Pennatulacea

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens.

Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics

Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.

The complete mitochondrial genome of soft coral Sinularia penghuensis Ofwegen and Benayahu, 2012 (Octocorallia: Alcyonacea): the analysis of mitogenome organization and phylogeny

The complete mitochondrial genome of Sinularia penghuensis was sequenced and analyzed using next-generation sequencing. The present mitochondrial genome was 18730 bp in length, containing 14 protein-coding genes (PCGs) (cox1-cox3.nad1-nad6, nad4L, atp6, atp8, cytb, and MutS), two ribosomal RNA genes (rRNAs) (12S and 16S), and one transfer RNA gene (Met-tRNA). The phylogenetic analysis of family Alcyoniidae revealed that S. penghuensis and Sinularia maxima cluster together. Five species in Sinularia reveals high identity in mitogenome sequences that the lowest variable sites (SNPs) were found between S. penghuensis and S. maxima.

Complete mitochondrial genome of Carijoa riisei (Duchassaing & Michelotti, 1860) (Octocorallia: Alcyonacea: Stolonifera: Clavulariidae)

We report the first complete Stoloniferamitochondrial genome.Carijoa riisei(Duchassaing&Michelotti, 1860) isolate CLP2_A03was collected by scuba at 32 m on the USTS Texas Clipper (27° 53.7827' N, 93° 36.2702' W). The complete mitogenome has the ancestral octocoral gene order for its 14 protein-coding genes, two rRNA genes, and one tRNA gene. It is 18,714 bp (30.7% A, 15.8% C, 18.8% G, and 34.7% T). Of the Alcyonacea mitogenomes published to date, it is most genetically similar (94% uncorrected) to Sinularia ceramensisVerseveldt, 1977 (NC_044122).

Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria

Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.

Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species-Leptogorgia virgulata and Leptogorgia hebes-from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil-calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.

Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System

Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.

The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum (Cnidaria: Anthozoa) using next-generation sequencing

The complete mitochondrial genome of Sarcophyton trocheliophorum was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,508 bp in length, containing 14 protein-coding genes, two ribosomal RNA genes and one transfer RNA gene (Met-tRNA). The base composition is 30.45% A, 16.03% C, 19.13% G, and 34.40% T, with an A + T content of 64.85%. A phylogenetic analysis of Alcyoniidae showed that genus Sarcophyton had the closest relationship with Sinularia.

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

Background

Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation.

Methodology

We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared.

Results

P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs.

Conclusion

This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia)

We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.

A review of gorgonian coral species (Cnidaria, Octocorallia, Alcyonacea) held in the Santa Barbara Museum of Natural History research collection: focus on species from Scleraxonia, Holaxonia, and Calcaxonia - Part I: Introduction, species of Scleraxonia and Holaxonia (Family Acanthogorgiidae)

Gorgonian specimens collected from the California Bight (northeastern Pacific Ocean) and adjacent areas held in the collection of the Santa Barbara Museum of Natural History (SBMNH) were reviewed and evaluated for species identification; much of this material is of historic significance as a large percentage of the specimens were collected by the Allan Hancock Foundation (AHF) 'Velero' Expeditions of 1931-1941 and 1948-1985. Examination and reorganization of this collection began early in 2002; initially, it was estimated that at most, twelve to fifteen species of gorgonian could be found within the Bight. Following collection evaluation, it was determined that at a minimum, approximately twenty three genera, encompassing some forty-plus species, of gorgonian coral have been found living within the California Bight region, often extending some distance into adjacent geographical areas both north and south. All species from the California Bight in the collection are discussed to some degree (in three separate parts, this being Part I), with digital images of both colony form and sclerite composition provided for most. Collection specimens from the suborders and families covered in Part I are not extensive, but several genera are featured that have not been previously reported for the California Bight region. Additionally, a potential new species (genus Sibogagorgia Stiasny, 1937) from the Paragorgiidae is described in Part I. Overall, the collection displays an emphasis on species belonging to the Holaxonia, particularly the plexaurids. A brief discussion of a California Bight grouping, referred to as the "red whips," is presented in Part II; this grouping encompasses several species with very similar colony appearance across a number of genera. A new species (a whip or thread-like form) in the genus Eugorgia Verrill, 1868, belonging to the Gorgoniidae, is described in Part II. The genus Swiftia Duchassaing & Michelotti, 1864 is one of the most challenging taxon groups represented; those species in the genus Swiftia collected within the California Bight are discussed fully, based on SBMNH (and other) specimens in Part III. Scanning electron microscopy images for species of Swiftia from the California coast have rarely, if ever, been published and are included, with a discussion of the geographic range of the genus in the eastern Pacific, from the southern boundary of the California Bight to the Bering Sea, Alaska. Finally, specimens of the genus Thesea Duchassaing & Michelotti, 1860, displaying a whip or thread-like body form, are discussed at a preliminary level in Part III; they also presented challenges to a clear understanding of their taxonomy. While Part I focuses on species of Scleraxonia and those of the Holaxonia in the Acanthogorgiidae family held in the SBMNH collection, all three parts taken together represent the first comprehensive work that reviews the research collection of SBMNH, which focuses on species of gorgonian coral known to inhabit the California Bight.

High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.

De novo transcriptome assembly of the digitate morphotype of Briareum asbestinum (Octocorallia: Alcyonacea) from the southwest shelf of Puerto Rico

Octocorals have now become the most visually dominant metazoan benthic taxa of most Caribbean reefs, following the precipitous decline of scleractinian corals. Yet taxonomic issues because of their extensive phenotypic plasticity are still abound. Briareum asbestinum one of the iconic octocorals of the shallow Caribbean coral reefs exhibits a biform morphology, the digitate and the encrusting one. The taxonomic status of each form has not been clarified, yet. Until recently, there were few genetic resources for non-model metazoans, however, affordable high-throughput DNA sequencing has removed this hindrance. We present the first transcriptome of the digitate form of Briareum asbestinum from southwest Puerto Rico. We used paired-end sequencing (Illumina NextSeq 500), with a total yield of 159,754,702 raw reads. De novo assembly was performed utilizing a multi-assembler approach generating 371,554 biologically true, non-redundant transcripts. Open reading frame analysis identified 102,839 putative ORFs of which 78,607 were with annotations. BUSCO analysis indicated a total of 96.4% complete orthologous genes from the metazoan dataset. The assembly presented here serves as an important new genomic reference for the Briareum genus that will facilitate future population and phylogenetic studies aiming to better understand the molecular basis of phenotypic plasticity exhibited throughout the genus.

Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNA^Met and tRNA^Trp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNA^Trp in Octocorallia.

Transcriptome analysis of the reef-building octocoral, Heliopora coerulea

The blue coral, Heliopora coerulea, is a reef-building octocoral that prefers shallow water and exhibits optimal growth at a temperature close to that which causes bleaching in scleractinian corals. To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. Metatranscriptome assembly yielded 90,817 sequences of which 71% (64,610) could be annotated by comparison to public databases. The assembly included transcript sequences from both the coral host and its symbionts, which are related to the thermotolerant C3-Gulf ITS2 type Symbiodinium. Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. Furthermore, the blue coral possesses homologs of biomineralization genes found in other corals and may use a biomineralization strategy similar to that of scleractinians to build its massive aragonite skeleton. These findings thus offer insights into the ecology of H. coerulea and suggest gene networks that may govern its interactions with its environment.

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species.

Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae)

Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

BACKGROUND

Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals.

RESULTS

We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected.

CONCLUSIONS

Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.

Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages

Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.

Phylogenetic reconstruction of scleraxonian octocorals supports the resurrection of the family Spongiodermidae (Cnidaria, Alcyonacea)

The Scleraxonia are a group of octocorals that share similarities of their axis morphology. However, molecular phylogenetic analyses have shown this group to be largely polyphyletic. As a result, there is a significant lack of understanding of what constitutes distinct evolutionary units among members of this group, particularly at the family level. Prompted by the discovery of an unknown spongiodermid scleraxonian octocoral (Anthothelidae) from shallow water off the Pacific coast of lower Baja California, a phylogenetic analysis of the undescribed specimen, together with members of six scleraxonian families and an additional 29 non-scleraxonian octocorallian families was performed. Two mitochondrial loci (mtMutS and COI) and one nuclear locus (28S) supported a monophyletic spongiodermid clade (Homophyton, Callipodium, Diodogorgia, Titanideum and Sclerophyton, gen. nov.) at the family-level. The unknown scleraxonian was supported as a new genus and species within the spongiodermid clade, sister to the western Atlantic genus Titanideum. A morphological examination of the taxa within this clade revealed shared morphological similarities in solenial (boundary) canals, and medullar and cortical sclerites. A revision, with illustrations, of the Spongiodermidae was performed. Similar to previous studies, this study underscores the importance of combined morphological and molecular analyses in order to resolve unstable systematic relationships among octocorals.