Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase

Complete mitochondrial genomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae)

We describe the complete mitogenomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1790) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). The analysed specimens include the holotype of Alternatipathesmirabilis, collected from Derickson Seamount (North Pacific Ocean; Gulf of Alaska) at 4,685 m depth and a potential topotype of Parantipatheslarix, collected from Secca dei Candelieri (Mediterranean Sea; Tyrrhenian Sea; Salerno Gulf; Italy) at 131 m depth. We also assemble, annotate and make available nine additional black coral mitogenomes that were included in a recent phylogeny (Quattrini et al. 2023b), but not made easily accessible on GenBank. This is the first study to present and compare two mitogenomes from the same species of black coral (Stauropathesarctica (Lütken, 1871)) and, thus, place minimum boundaries on the expected level of intraspecific variation at the mitogenome level. We also compare interspecific variation at the mitogenome-level across five different specimens of Parantipathes Brook, 1889 (representing at least two different species) from the NE Atlantic and Mediterranean Sea.

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.

Confirmation of the first intronic sequence in the bivalvian mitochondrial genome of Macoma balthica (Linnaeus, 1758)

In 2020, the first male-type mitochondrial genome from the clam Macoma balthica was published. Apart from the unusual doubly uniparental inheritance of mtDNA, scientists observed a unique (over 4k bp long) extension in the middle of the cox2 gene. We have attempted to replicate these data by NGS DNA sequencing and explore further the expression of the long cox2 gene. In our study, we report an even longer cox2 gene (over 5.5 kbp) with no stop codon separating conserved cox2 domains, as well as, based on the rtPCR, a lower relative gene expression pattern of the middle part of the gene (5' = 1; mid = 0.46; 3' = 0.89). Lastly, we sequenced the cox2 gene transcript proving the excision of the intronic sequence.

Unprecedented frequency of mitochondrial introns in colonial bilaterians

Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.

Comparative Analysis of the Mitochondrial Genome of Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae) From a Depth of 9,462 m at the Mariana Trench

The hadal zone, which represents the deepest marine habitat on Earth (6,000–11,000 m), is a harsh environment mainly characterized by extremely high hydrostatic pressure, and this habitat is believed to have a high degree of endemism. The deep-sea anemone family Galatheanthemidae comprises two valid species exclusively from the hadal; however, no other information about this family is currently available. In the present study, a sea anemone was collected from a depth of 9,462 m at the Mariana Trench and was defined as Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae). The mitochondrial genome of Galatheanthemum sp. MT-2020 was circular, was 16,633 bp in length, and contained two ribosomal RNA genes, 13 protein-coding genes and two transfer RNA genes. The order of the genes of Galatheanthemum sp. MT-2020 was identical to that of the majority of the species of the order Actiniaria. The value of the AT-skew was the lowest in the whole mitochondrial genome, with a positive GC skew value for the atp8 gene, while other species, except Antholoba achates, had the negative values of the GC skew. Galatheanthemum sp. MT-2020 was clustered with another abyssal species, Paraphelliactis xishaensis, in the phylogenetic tree, and these species diverged in the early Jurassic approximately 200 Mya from the shallow-sea species. The usage ratio of valine, which is one of the five amino acids with the strongest barophilic properties, in the mitochondrial genomes of the two abyssal species was significantly higher than that in other species with habitats above the depth of 3,000 m. The ω (dN/dS) ratio of the genomes was 2.45-fold higher than that of the shallow-sea species, indicating a slower evolutionary rate. Overall, the present study is the first to provide a complete mitogenome of sea anemones from the hadal and reveal some characteristics that may be associated with adaptation to an extreme environment.

Organellar Introns in Fungi, Algae, and Plants

Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny

A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.

The first mitochondrial genome of scale insects (Hemiptera: Coccoidea)

Here, we report the first mitochondrial genome of scale insects sequenced from Ceroplastes japonicus (Hemiptera: Coccidae). The genome has a circular genome of 14,979 bp in length, with a high A + T content of 85.15%. Twelve protein-coding genes (excluding atp8), 13 tRNA, and 2 rRNA genes were detected and annotated using the MITOS web server. The absence of atp8 and some tRNAs might indicate possible novel structures or loss of genes.

Giant group I intron in a mitochondrial genome is removed by RNA back-splicing

Background

The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA.

Results

We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer. All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma, respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment.

Conclusion

ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns.

Electronic supplementary material

The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.

Deep-water sea anemone with a two-chromosome mitochondrial genome

Mitochondrial genome organization of sea anemones appears conserved among species and families, and is represented by a single circular DNA molecule of 17 to 21 kb. The mitochondrial gene content corresponds to the same 13 protein components of the oxidative phosphorylation (OxPhos) system as in vertebrates. Hallmarks, however, include a highly reduced tRNA gene repertoire and the presence of autocatalytic group I introns. Here we demonstrate that the mitochondrial genome of the deep-water sea anemone Protanthea simplex deviates significantly from that of other known sea anemones. The P. simplex mitochondrial genome contains a heavily scrambled order of genes that are coded on both DNA strands and organized along two circular mito-chromosomes, MCh-I and MCh-II. We found MCh-I to be representative of the prototypic sea anemone mitochondrial genome, encoding 12 OxPhos proteins, two ribosomal RNAs, two transfer RNAs, and a group I intron. In contrast, MCh-II was found to be a laterally transferred plasmid-like DNA carrying the conserved cytochrome oxidase II gene and a second allele of the small subunit ribosomal RNA gene.

The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?

BACKGROUND

Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2-3 tRNA genes was reported in Tyrophagus longior, T. putrescentiae and Sarcoptes scabiei. Nevertheless, convincing evidence for mt gene loss is lacking in these mites.

RESULTS

We sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini, respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus, two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae, and the two mt tRNA genes that were reported as lost in Sa. scabiei. All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems.

CONCLUSIONS

Our results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.

Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: Lesson learned from Anemonia viridis

The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function.

Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome

Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment

The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.

Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa)

Yaoyang Chuang, Marcelo Kitahara, Hironobu Fukami, Dianne Tracey, David J. Miller, and Chaolun Allen Chen (2017) Group I introns encoding a homing endonuclease gene (HEG) that is potentially capable of sponsoring mobility are present in the cytochrome oxidase subunit 1 (cox1) gene of some Hexacorallia, including a number of scleractinians assigned to the "robust" coral clade. In an e ort to infer the evolutionary history of this cox1 group I intron, DNA sequences were determined for 12 representative "basal" and "complex" corals and for 11 members of the Corallimorpharia, a sister order of the Scleractinia. Comparisons of insertion sites, secondary structures, and amino acid sequences of the HEG implied a common origin for cox1 introns of corallimorpharians, and basal and complex corals, but cox1 introns of robust corals were highly divergent, most likely reflecting independent acquisition. Phylogenetic analyses with a calibrated molecular clock suggested that cox1 introns of scleractinians and corallimorpharians have persisted at the same insertion site as that in the common ancestor 552 million years ago (mya). This ancestral intron was probably lost in complex corals around 213 to 190 mya at the junction between the Trassic and Jurassic. The coral cox1 gene remained intronless until new introns, probably from sponges or fungi, reinvaded different positions of the cox1 gene in robust corals around 135 mya in the Cretaceous, and then it subsequently began to lose them around 65.5 mya in some robust coral lineages coincident with the later Maastrichtian extinction at the Cretaceous-Tertiary boundary.

Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia)

Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as ‘homing’. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (K_a) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower K_a rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals.

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.

A mitochondrial intron in a verongid sponge

We discovered for the first time a mitochondrial intron in a non-tetillid demosponge, which sheds new light on the interpretation of mitochondrial intron evolution among non-bilaterian animals and has consequences for phylogenetic and DNA barcoding studies. The newly discovered class 1 intron of Aplysinella rhax (Verongida) CO1 has an ORF for a putative LAGLIDADG-type and resembles other sponge and cnidarian mitochondrial introns. Our analysis of the Aplysinella rhax intron underlines that the patchy distribution of introns in sponges is caused by a combination of horizontal and vertical transmission. Further implications for CO1 phylogenetic and barcoding projects are discussed.

Characterization and localization of mitochondrial DNA-encoded tRNAs and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile

The mitochondrial (mt) genome of the sea anemone Metridium senile contains genes for only two transfer RNAs (tRNAs), tRNAf-Met and tRNATrp. Experiments were conducted to seek evidence for the occurrence of functional tRNAs corresponding to these genes and for the participation of nuclear DNA-encoded tRNAs in mt-protein synthesis. RNA sequences corresponding to the two mt-tRNA genes were located in mitochondria and it was shown that 3'-CC (and possibly A, but no other nucleotide) is added post-transcriptionally to the 3' end of at least 50 % of mt-tRNAf-Met molecules and to a small fraction of the mt-tRNATrp molecules. Using specific oligonucleotide primers based on expected nuclear DNA-encoded tRNAs in a series of RACE experiments, we located the nuclear genes for tRNAGln, tRNAIle, tRNAi-Met, tRNAVal and tRNAThr. Data from Northern blot analyses indicated that mtDNA-encoded tRNAf-Met is limited to mitochondria but that nuclear DNA-encoded tRNAVal and tRNAi-Met are present in the cytoplasm and in mitochondria. These data provide direct evidence that in M. senile, mature, functional tRNAs are transcribed from the mtDNA-encoded tRNAf-Met and tRNATrp genes, and are consistent with the interpretation that both nuclear DNA-encoded tRNAVal and tRNAi-Met are utilized in mitochondrial and cytosolic protein synthesis.

Genetic aspects of mitochondrial genome evolution

Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.

The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes

Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.

MITOS: improved de novo metazoan mitochondrial genome annotation

About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.

Selfish little circles: transmission bias and evolution of large deletion-bearing mitochondrial DNA in Caenorhabditis briggsae nematodes

Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ mtDNA using eight sets of C. briggsae mutation-accumulation (MA) lines, each initiated from a different natural strain progenitor and bottlenecked as single hermaphrodites across generations. We observed a consistent and strong drive toward higher levels of deletion-bearing molecules in the heteroplasmic pool of mtDNA after ten generations of bottlenecking. Our results demonstrate a uniform transmission bias whereby nad5Δ mtDNA accumulates to higher levels relative to intact mtDNA in multiple genetically diverse natural strains of C. briggsae. We calculated an average 1% per-generation transmission bias for deletion-bearing mtDNA relative to intact genomes. Our study, coupled with known deleterious phenotypes associated with high deletion levels, shows that nad5Δ mtDNA are selfish genetic elements that have evolved in natural populations of C. briggsae, offering a powerful new system to study selfish mtDNA dynamics in metazoans.

The rhizome of life: what about metazoa?

The increase in huge number of genomic sequences in recent years has contributed to various genetic events such as horizontal gene transfer (HGT), gene duplication and hybridization of species. Among them HGT has played an important role in the genome evolution and was believed to occur only in Bacterial and Archaeal genomes. As a result, genomes were found to be chimeric and the evolution of life was represented in different forms such as forests, networks and species evolution was described more like a rhizome, rather than a tree. However, in the last few years, HGT has also been evidenced in other group such as metazoa (for example in root-knot nematodes, bdelloid rotifers and mammals). In addition to HGT, other genetic events such as transfer by retrotransposons and hybridization between more closely related lineages are also well established. Therefore, in the light of such genetic events, whether the evolution of metazoa exists in the form of a tree, network or rhizome is highly questionable and needs to be determined. In the current review, we will focus on the role of HGT, retrotransposons and hybridization in the metazoan evolution.

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

Background

The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular systematics, due to its high information content. Several hypotheses concerning the origins of mtMutS have been proposed, and remain equivocal, although current weight of support is for a horizontal gene transfer from either an epsilonproteobacterium or a large DNA virus. Here we present new and compelling evidence on the evolutionary origin of mtMutS, and provide the very first data on its activity, functional capacity and stability within the octocoral mitochondrial genome.

Results

The mtMutS gene has the expected conserved amino acids, protein domains and predicted tertiary protein structure. Phylogenetic analysis indicates that mtMutS is not a member of the MSH family and therefore not of eukaryotic origin. MtMutS clusters closely with representatives of the MutS7 lineage; further support for this relationship derives from the sharing of a C-terminal endonuclease domain that confers a self-contained mismatch repair function. Gene expression analyses confirm that mtMutS is actively transcribed in octocorals. Rates of mitochondrial gene evolution in mtMutS-containing octocorals are lower than in their hexacoral sister-group, which lacks the gene, although paradoxically the mtMutS gene itself has higher rates of mutation than other octocoral mitochondrial genes.

Conclusions

The octocoral mtMutS gene is active and codes for a protein with all the necessary components for DNA mismatch repair. A lower rate of mitochondrial evolution, and the presence of a nicking endonuclease domain, both indirectly support a theory of self-sufficient DNA mismatch repair within the octocoral mitochondrion. The ancestral affinity of mtMutS to non-eukaryotic MutS7 provides compelling support for an origin by horizontal gene transfer. The immediate vector of transmission into octocorals can be attributed to either an epsilonproteobacterium in an endosymbiotic association or to a viral infection, although DNA viruses are not currently known to infect both bacteria and eukaryotes, nor mitochondria in particular. In consolidating the first known case of HGT into an animal mitochondrial genome, these findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve.

The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication

Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals.

Cordyceps militaris (Hypocreales: Cordycipitaceae): transcriptional analysis and molecular characterization of cox1 and group I intron with putative LAGLIDADG endonuclease

The full-length cytochrome c oxidase subunit I gene (cox1) containing a group I intron was isolated from an important medical fungus Cordyceps militaris (Cordycipitaceae). The open reading frame (ORF) of 1,593 nucleotides encoded a predicted protein COX1 of 530 amino acids. The group I intron encoded a putative homing endonuclease (HE) with two LAGLIDADG motifs. RT-PCR and Northern analysis showed a mature transcript of spliced cox1. Both 5'exon-intron and intron-3'exon junctions were also found by RT-PCR, suggesting the possible presence of unspliced cox1 RNA in total RNA. Sequence comparison by BLASTn showed that the coding region of cox1 (CRcox1) of C. militaris had significant similarities to those of related species (such as Cordyceps bassiana and C. brongniartii), while the intron had no significant homologous sequences of Cordycipitaceae fungi in NCBI database. The phylogenetic tree based on the CRcox1 confirmed the present taxonomic status of related species, but the cox1 introns were phylogenetically distinct. Compared to C. bassiana and C. brongniartii, the cox1 intron of C. militaris exhibited specific splicing site and different intronic ORF. The analysis of the folding RNA structures of the known cox1 introns from Cordyceps species showed different base pairs and conserved regions (P1-P10) in their structures. The present results provide useful information on the studies of cox1 intron splicing and Cordyceps evolution.

The making of a photosynthetic animal

Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO(2) fixation (photosynthesis). 'Solar-powered' sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a 'plant' when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ~10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating 'green animal' provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism.

Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae

Background

Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family.

Results

Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant.

Conclusions

The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the cox 1 topologies. In addition, our results suggest that three different intron forms independently colonized the cox 1 gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.

A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii

Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombination events, and chloroplast as well as nuclear DNA inserts document the incorporation of foreign sequences already in this most ancestral vascular plant lineage. On the other hand, particularly small group II introns and short intergenic regions reveal a tendency of evolution towards a compact mitochondrial genome. RNA editing reaches extreme levels exceeding 100 pyrimidine exchanges in individual mRNAs and, hitherto unobserved in such frequency, also in tRNAs with 18 C-to-U conversions in the tRNA for proline. In total, some 1500 sites of RNA editing can be expected for the Isoetes mitochondrial transcriptome. As a unique molecular novelty, the Isoetes cox1 gene requires trans-splicing via a discontinuous group I intron demonstrating disrupted, but functional, RNAs for yet another class of natural ribozymes.

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3' flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty ("green animals") and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.

Unique mitogenomic features in the scleractinian family pocilloporidae (scleractinia: astrocoeniina)

The complete DNA sequences of three mitochondrial (mt) genomes were obtained from the scleractinian corals, Stylophora pistillata, Pocillopora damicornis, and Madracis mirabilis, and were compared to the published mt genomes to elucidate phylogenetically unique features of the family Pocilloporidae. The entire mt genomes of pocilloporid corals ranged from 16,951 to 17,425 bp with the A+T contents of their sense strands ranging from 68.4% to 70.2%. The gene order of protein-coding genes was identical to those of other scleractinian corals. The novel atp8 gene, first described in confamilial Seriatopora corals, was also confirmed using reverse transcription-polymerase chain reaction (RT-PCR), Northern blot, and sequence analyses in other genera of the Pocilloporidae. The intergenic spacer between atp6 and nad4, containing distinct repeated elements, conserved sequence blocks and domains, and functional structures, possesses typical characteristics of a putative control region for the four coral genera. A duplicated trnW, detected in the region close to the cox1 gene and which shares the highly conserved primary and secondary structures of its original counterpart, was discovered in both Seriatopora and Stylophora. These molecular characteristics are unique and provide the phylogenetic information for future evaluation of the status of the family Pocilloporidae in the evolutionary history of scleractinian corals.

The future biological control of pest populations of European rabbits, Oryctolagus cuniculus

European rabbits are exotic pests in Australia, New Zealand, parts of South America and Europe, and on many islands. Their abundance, and the damage they cause, might be reduced by the release of naturally occurring or genetically modified organisms (GMOs) that act as biological control agents (BCAs). Some promising pathogens and parasites of European rabbits and other lagomorphs are discussed, with special reference to those absent from Australia as an example of the range of necessary considerations in any given case. The possibility of introducing these already-known BCAs into areas where rabbits are pests warrants further investigation. The most cost-effective method for finding potentially useful but as-yet undiscovered BCAs would be to maintain a global watch on new diseases and pathologies in domestic rabbits. The absence of wild European rabbits from climatically suitable parts of North and South America and southern Africa may indicate the presence there of useful BCAs, although other explanations for their absence are possible. Until the non-target risks of deploying disseminating GMOs to control rabbits have been satisfactorily minimised, efforts to introduce BCAs into exotic rabbit populations should focus on naturally occurring organisms. The development of safe disseminating GMOs remains an important long-term goal, with the possible use of homing endonuclease genes warranting further investigation.

An assessment of potential diatom "barcode" genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta)

Due to limited morphological differentiation, diatoms can be very difficult to identify and cryptic speciation is widespread. There is a need for a narrower species concept if contentious issues such as diatom biodiversities and biogeographies are to be resolved. We assessed the effectiveness of several genes (cox1, rbcL, 18S and ITS rDNA) to distinguish cryptic species within the model 'morphospecies', Sellaphora pupula agg. This is the first time that the suitability of cox1 as an identification tool for diatoms has been assessed. A range of cox1 primers was tested on Sellaphora and various outgroup taxa. Sequences were obtained for 34 isolates belonging to 22 Sellaphora taxa and three others (Pinnularia, Eunotia and Tabularia). Intraspecific divergences ranged from 0 to 5bp (=0.8%) and interspecific levels were at least 18bp (=c. 3%). Cox1 divergence was usually much greater than rbcL divergence and always much more variable than 18S rDNA. ITS rDNA sequences were more variable than cox1, but well-known problems concerning intragenomic variability caution against its use in identification. More information and less sequencing effort mean that cox1 can be a very useful aid in diatom identification. The usefulness of cox1 for determining phylogenetic relationships among Sellaphora species was also assessed and compared to rbcL. Tree topologies were very similar, although support values were generally lower for cox1.

Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of Scleractinian corals

Analyses of mitochondrial sequences revealed the existence of a group I intron in the cytochrome oxidase subunit 1 (cox1) gene in 13 of 41 genera (20 out of 73 species) of corals conventionally assigned to the suborder Faviina. With one exception, phylogenies of the coral cox1 gene and its intron were concordant, suggesting at most two insertions and many subsequent losses. The coral introns were inferred to encode a putative homing endonuclease with a LAGLI-DADG motif as reported for the cox1 group I intron in the sea anemone Metridium senile. However, the coral and sea anemone cox1 group I introns differed in several aspects, such as the intron insertion site and sequence length. The coral cox1 introns most closely resemble the mitochondrial cox1 group I introns of a sponge species, which also has the same insertion site. The coral introns are also more similar to the introns of several fungal species than to that of the sea anemone (although the insertion site differs in the fungi). This suggests either a horizontal transfer between a sponge and a coral or independent transfers from a similar fungal donor (perhaps one with an identical insertion site that has not yet been discovered). The common occurrence of this intron in corals strengthens the evidence for an elevated abundance of group I introns in the mitochondria of anthozoans.

Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny

Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.

Invasion and persistence of a selfish gene in the Cnidaria

Background

Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising.

Methods/Principal Findings

We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution.

Conclusions

Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion.

Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase

The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.

Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria

BACKGROUND

The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera).

RESULTS

A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor.

CONCLUSION

Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.

Naked corals: skeleton loss in Scleractinia

Stony corals, which form the framework for modern reefs, are classified as Scleractinia (Cnidaria, Anthozoa, and Hexacorallia) in reference to their external aragonitic skeletons. However, persistent notions, collectively known as the "naked coral" hypothesis, hold that the scleractinian skeleton does not define a natural group. Three main lines of evidence have suggested that some stony corals are more closely related to one or more of the soft-bodied hexacorallian groups than they are to other scleractinians: (i) morphological similarities; (ii) lack of phylogenetic resolution in molecular analyses of scleractinians; and (iii) discrepancy between the commencement of a diverse scleractinian fossil record at 240 million years ago (Ma) and a molecule-based origination of at least 300 Ma. No molecular evidence has been able to clearly reveal relationships at the base of a well supported clade composed of scleractinian lineages and the nonskeletonized Corallimorpharia. We present complete mitochondrial genome data that provide strong evidence that one clade of scleractinians is more closely related to Corallimorpharia than it is to a another clade of scleractinians. Thus, the scleractinian skeleton, which we estimate to have originated between 240 and 288 Ma, was likely lost in the ancestry of Corallimorpharia. We estimate that Corallimorpharia originated between 110 and 132 Ma during the late- to mid-Cretaceous, coinciding with high levels of oceanic CO(2), which would have impacted aragonite solubility. Corallimorpharians escaped extinction from aragonite skeletal dissolution, but some modern stony corals may not have such fortunate fates under the pressure of increased anthropogenic CO(2) in the ocean.

The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes

The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present.

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective

Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.