Cox1 Intron Research Articles

Mitochondrial DNA of the demosponge Acanthella acuta: Linear Architecture and Other Unique Features.

While Acanthella acuta (Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is-morphologically-little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, mtDNA of A. acuta is inferred to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.

Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene.

The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.

Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii.

The species complexes Cryptococcus neoformans and Cryptococcus gattii are the causative agents of cryptococcosis. Virulence and susceptibility to antifungals may vary within each species according to the fungal genotype. Therefore, specific and easily accessible molecular markers are required to distinguish cryptic species and/or genotypes. Group I introns are potential markers for this purpose because they are polymorphic concerning their presence and sequence. Therefore, in this study, we evaluated the presence of group I introns in the mitochondrial genes cob and cox1 in different Cryptococcus isolates. Additionally, the origin, distribution, and evolution of these introns were investigated by phylogenetic analyses, including previously sequenced introns for the mtLSU gene. Approximately 80.5% of the 36 sequenced introns presented homing endonucleases, and phylogenetic analyses revealed that introns occupying the same insertion site form monophyletic clades. This suggests that they likely share a common ancestor that invaded the site prior to species divergence. There was only one case of heterologous invasion, probably through horizontal transfer to C. decagattii (VGIV genotype) from another fungal species. Our results showed that the C. neoformans complex has fewer introns compared to C. gattii. Additionally, there is significant polymorphism in the presence and size of these elements, both among and within genotypes. As a result, it is impossible to differentiate the cryptic species using a single intron. However, it was possible to differentiate among genotypes within each species complex, by combining PCRs of mtLSU and cox1 introns, for C. neoformans species, and mtLSU and cob introns for C. gattii species.

Complete mitochondrial genomes of two species of Stichopathes Brook, 1889 (Hexacorallia: Antipatharia: Antipathidae) from Rapa Nui (Easter Island)

We report the complete mitochondrial genomes of two antipatharian species, Stichopathes sp. SCBUCN-8849 and Stichopathes sp. SCBUCN-8850, collected between 120 and 180 m depth off Rapa Nui (∼ −27.1°, −109.4°). The size of the two mitogenomes are 20,389 bp (29.0% A, 15.2% C, 19.9% G, and 35.9% T) and 20,463 bp (29.0% A, 15.3% C, 19.9% G, and 35.8% T), respectively. Both mitogenomes have the classic Hexacorallia gene content of 13 protein-coding, two rRNA, and two tRNA genes plus a COX1 intron with embedded HEG as found in the Antipathidae and other antipatharian families.

Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake.

Fungi, as eukaryotic organisms, contain two genomes, the mitochondrial genome and the nuclear genome, in their cells. How the two genomes evolve and correlate to each other is debated. Herein, taking the gourmet pine mushroom Tricholoma matsutake as an example, we performed comparative mitogenomic analysis using samples collected from diverse locations and compared the evolution of the two genomes. The T. matsutake mitogenome encodes 49 genes and is rich of repetitive and non-coding DNAs. Six genes were invaded by up to 11 group I introns, with one cox1 intron cox1P372 showing presence/absence dynamics among different samples. Bioinformatic analyses suggested limited or no evidence of mitochondrial heteroplasmy. Interestingly, hundreds of mitochondrial DNA fragments were found in the nuclear genome, with several larger than 500 nt confirmed by PCR assays and read count comparisons, indicating clear evidence of transfer of mitochondrial DNA into the nuclear genome. Nuclear DNA of T. matsutake showed a higher mutation rate than mitochondrial DNA. Furthermore, we found evidence of incongruence between phylogenetic trees derived from mitogenome and nuclear DNA sequences. Together, our results reveal the dynamic genome evolution of the gourmet pine mushroom.

Complete plastome phylogeny and an update on cox1 intron evolution of Hyoscyameae (Solanaceae)

Within the family Solanaceae, the tribe Hyoscyameae comprises eight genera distributed across Eurasia. Despite a few attempts to understand the relationships within this tribe, the affiliations among most genera remain unresolved. Recently, complete chloroplast genomes from several species of Hyoscyameae were published, enabling phylogenomic inferences. We sequenced the plastome of Scopolia carniolica, the second species of the genus to be reported. Genomic comparisons across the tribe revealed identical gene content and small differences in genome length. Phylogenetic analyses confirmed that Atropa is an early-diverging lineage sister to the rest of the tribe, resolved as two clades. One includes well-supported relationships between Przewalskia, Physochlaina, and Scopolia, and these three genera are sister to Atropanthe. This clade is sister to a second clade composed of Hyoscyamus and Anisodus. The strongly supported phylogenetic affiliations of Atropanthe, Anisodus, and Hyoscyamus represent the major advancements as previous studies were not able to resolve these relationships. Interestingly, the genus Scopolia is paraphyletic in respect to Physochlaina, based on ITS2 sequences. Finally, the evolution of the mitochondrial cox1 intron is reinterpreted. Two independent horizontal acquisitions are inferred, one in the ancestor of Przewalskia, Physochlaina, and S. japonica and another in Hyoscyamus, with no intron losses.

Complete mitochondrial genome of Polyopes lancifolius and comparison with related species in Halymeniales (Rhodophyta)

Polyopes lancifolius is a species of Halymeniales, the fifth species-rich order within Rhodophyta. Using next-generation sequencing techniques, we recovered the complete mitochondrial genome of P. lancifolius, i.e. total 26,142 bp in length with 31% GC contents. A total of 49 functional genes were annotated, including 24 protein-coding, 23 transfer RNA, and 2 ribosomal RNA genes. The gene content and synteny have been highly congruent to those of the other halymenialean species, such as Grateloupia taiwanensis, G. filicina, and Grateloupia angusta. Interestingly, the cox1 intron and intronic Open Reading Frame (ORF) are absent in P. lancifolius, that are existed in the other three halymenialean species.

Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation.

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III2 were also observed in nodules, although the causal relationship between these observations requires further investigation.

Phylogenetics and Mitogenome Organisation in Black Corals (Anthozoa: Hexacorallia: Antipatharia): An Order-Wide Survey Inferred From Complete Mitochondrial Genomes

Black corals (Anthozoa: Antipatharia) are an ecologically and culturally important group of deep-sea cnidarians. However, as the majority of species inhabit depths >50 m, they are relatively understudied. The inaccessibility of well-preserved tissue for species of interest has limited the scope of molecular analysis, and as a result only a small number of antipatharian mitochondrial genomes have been published. Using next generation sequencing, eighteen complete and five partial antipatharian mitochondrial genomes were assembled, increasing the number of complete mitochondrial genomes to twenty-two. This includes species from six antipatharian families, four of which were previously unrepresented, enabling the first family-level, full mitochondrial gene analysis over the whole order. The circular mitogenomes ranged in size from 17681 to 21669 bp with the large range in size due to the addition of an intron in COX1 in some species and size variation of intergenic regions. All mitogenomes contained the genes standard to all hexacoral mitogenomes (13 protein coding genes, two rRNAs and two tRNAs). The only difference in gene content is the presence of the COX1 intron in five families. The most variable mitochondrial gene is ND4 which may have implications for future barcoding studies. Phylogenetic analysis confirms that Leiopathidae is sister to all other families. Families Antipathidae, Cladopathidae and Schizopathidae are polyphyletic, supporting previous studies that call for a taxonomic revision.

Two Novel PLS-Class Pentatricopeptide Repeat Proteins Are Involved in the Group II Intron Splicing of Mitochondrial Transcripts in the Moss Physcomitrella patens.

Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5' region of nad5 exon 4 and the bulged A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that a certain set of PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.

Horizontal Gene Transfer has Impacted cox1 Gene Evolution in Cassytha filiformis.

The gene cox1 is one of the most reported mitochondrial genes involved in horizontal gene transfer among angiosperms. However, whether different cox1 copies exist in different populations of a species and whether any other novel way except intron homing exists for cox1 intron acquisition is less understood. In this study, we chose Cassytha filiformis, a parasitic plant from the angiosperm family Lauraceae, as an example to study cox1 variation and evolution. We identified the stable and inheritable co-occurrence of two copies of cox1 genes, which were different in base composition and insertion/deletion among samples of a single species, C. filiformis. The bioinformatic analyses revealed that Type I copy had intact open reading frames, but type II copy had premature stop codons and was a pseudogene. Further INDEL characterization, phylogenetic analyses, and CCT comparisons consistently support two different origins for the two types of C. filiformis cox1 genes. Type I cox1 was likely vertically inherited within the magnoliids but it has captured an intron from another species, whereas the entire type II intron-containing cox1 has most likely been transferred integrally from Cuscuta or other Convolvulaceae species. The finding of the two independent horizontal gene transfer events associated with C. filiformis cox1 genes not only promotes our understanding of the evolutionary history of C. filiformis, but also leaves intriguing evolutionary questions that merits further efforts.

Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)

Cnidarians are early-diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re-evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt-genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt-genomes of members of eight of nine zoantharian families. Although all examined mt-genomes had the same gene order arrangement, there were variations among mt-genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt-DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt-genome protein-coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher-level phylogeny and taxonomy of Zoantharia.

Scleractinian corals from the upper Berriasian of central Europe and comparison with contemporaneous coral assemblages.

Scleractinian coral faunas from the upper Berriasian part of the Oehrli Formation of western Austria (Vorarlberg) and eastern Switzerland (Canton of Appenzell) are taxonomically described for the first time. Furthermore, scleractinian corals of the upper Berriasian part of the Oehrli Formation of the Swiss Cantons of Nidwalden and Uri are revised based on the study of type material. Lectotypes are designated for the species Dimorphocoeniopsis alpina (Koby, 1896) and Pleurophyllia tobleri (Koby, 1896). Sixty-one species belonging to 43 genera and 18 families were identified, making the coral fauna of the upper Oehrli Formation by far the most diverse among the Berriasian assemblages: Actinastrea pseudominima (Koby), A. sp., Adelocoenia bulgarica (Toula)(new combination), A. hexaphyllia (d'Orbigny)(new combination), A. radisensis (d'Orbigny)(new combination), Allocoeniopsis luciensis (d'Orbigny), Amphiaulastrea sp., Astraeofungia cf. decipiens (Michelin), Cladophyllia conybearei Milne Edwards Haime, Columnocoenia ksiazkiewiczi Morycowa, Comoseris jireceki Toula, Complexastrea seriata Turnšek, C. lobata Geyer, Cycloria mariscali (Felix)(new combination), Dermosmilia capitata (Koby), D. simplex Koby, Dimorphastrea excavata d'Orbigny, D. explanata De Fromentel, Dimorphocoeniopsis alpina (Koby), Ellipsocoenia lorioli (Koby), Enallhelia compressa (Münster), E. rathieri d'Orbigny, Epistreptophyllum cf. densum Roniewicz, Fungiastraea moeschi (Koby), Heliocoenia corallina Koby, H. humberti Étallon, H. minima Sikharulidze, Heterocoenia cf. inflexa (Eichwald), Latiphyllia neocomiensis De Fromentel, Latiastrea mucronata Sikharulidze, Latomeandra sp., Meandrastrea rudis (De Fromentel)(new combination), M. cf. lamberti (Bataller), Meandrophyllia corrugata (Michelin), Microsolena major (Ferry), M. cf. subexcavata Eguchi, Mitrodendron cf. modicum Eliášová, Mixastraea polyseptata Morycowa, Montlivaltia arcuata Beauvais, M. kaufmanni Koby, M. truncata (Defrance, 1817), Myriophyllia cf. propria Sikharulidze, Paraclausastrea vorarlbergensis Baron-Szabo, Peplosmilia stutzi (Koby), Placocoenia heimi (Koby)(new combination), Placophyllia dianthus (Goldfuss), Plesiomontlivaltia paucisepta (Koby)(new combination), Pleurophyllia schmidti (Koby)(new combination), P. tobleri (Koby), Polyphylloseris icaunensis (d'Orbigny, 1850), Rhipidogyra cf. minima Koby, Stylangia cf. laddi Wells, Stylina pleionantha Meneghini, S. decipiens Étallon, S. cf. sparsa Trautschold, Stylosmilia alpina Koby, S. yabei Eguchi, Thecosmilia dichotoma (Koby), Th. sp., Trigerastraea gourdani (De Fromentel), and Vallimeandra cf. explanata (De Fromentel). Furthermore, five additional Berriasian coral faunas are reviewed and compared with the coral fauna of the upper Oehrli Formation. These five assemblages are from southern Ukraine (2 assemblages, consisting of five and 12 species, respectively), northern Tunisia (13 species), southern Spain (23 species), and central Tibet (11 species). Except for the faunas from central Tibet and northern Tunisia, the Berriasian coral assemblages are distinctly dominated by colonial species (70-95%); they represent largely isolated populations of mostly endemic species; and consist largely of genera that had already appeared in the Upper Jurassic (80-100%). On the species-level, however, with the exception of the coral assemblage of Spain, the Beriasian coral faunas are dominated by or completely consist of taxa that have their first occurrence in the Berriasian (54-100%). The Berriasian fauna of the upper Oehrli Formation described in this work contains nearly three times more species than found in the contemporaneous fauna of southern Spain which up to now was the largest known Berriasian fauna. Two of the upper Berriasian taxa described in the current work (Cycloria and Placocoenia) may be the first representatives of lineages that still occur today (Mussidae and Montastraeidae, respectively) as suggested by a recent study of the cox1 Intron in modern corals.

Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon.

The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 (“Panama” clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.

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.

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae.

In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.

Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers.

The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G.brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.

The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae).

The tribe Hyoscyameae (Solanaceae) is restricted to Eurasia and includes the genera Archihyoscyamus, Anisodus, Atropa, Atropanthe, Hyoscyamus, Physochlaina, Przewalskia and Scopolia. Even though the monophyly of Hyoscyameae is strongly supported, the relationships of the taxa within the tribe remain unclear. Chloroplast markers have been widely used to elucidate plant relationships at low taxonomic levels. Identification of variable chloroplast intergenic regions has been developed based on comparative genomics of chloroplast genomes, but these regions have a narrow phylogenetic utility. In this study, we present the chloroplast genome sequence of Hyoscyamus niger and make comparisons to other solanaceous plastid genomes in terms of gene order, gene and intron content, editing sites, origins of replication, repeats, and hypothetical open reading frames. We developed and sequenced three variable plastid markers from eight species to elucidate relationships within the tribe Hyoscyameae. The presence of a horizontally transferred intron in the mitochondrial cox1 gene of some species of the tribe is considered here a likely synapomorphy uniting five genera of the Hyoscyameae. Alternatively, the cox1 intron could be a homoplasious character acquired twice within the tribe. A homoplasious inversion in the intergenic plastid spacer trnC-psbM was recognized as a source of bias and removed from the data set used in the phylogenetic analyses. Almost 12 kb of plastid sequence data were not sufficient to completely resolve relationships among genera of Hyoscyameae but some clades were identified. Two alternative hypotheses of the evolution of the genera within the tribe are proposed.

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333.

Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.

Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B.

BackgroundChorella is the representative taxon of Chlorellales in Trebouxiophyceae, and its chloroplast (cp) genomic information has been thought to depend only on studies concerning Chlorella vulgaris and GenBank information of C. variablis. Mitochondrial (mt) genomic information regarding Chlorella is currently unavailable. To elucidate the evolution of organelle genomes and genetic information of Chlorella, we have sequenced and characterized the cp and mt genomes of Arctic Chlorella sp. ArM0029B.ResultsThe 119,989-bp cp genome lacking inverted repeats and 65,049-bp mt genome were sequenced. The ArM0029B cp genome contains 114 conserved genes, including 32 tRNA genes, 3 rRNA genes, and 79 genes encoding proteins. Chlorella cp genomes are highly rearranged except for a Chlorella-specific six-gene cluster, and the ArM0029B plastid resembles that of Chlorella variabilis except for a 15-kb gene cluster inversion. In the mt genome, 62 conserved genes, including 27 tRNA genes, 3 rRNA genes, and 32 genes encoding proteins were determined. The mt genome of ArM0029B is similar to that of the non-photosynthetic species Prototheca and Heicosporidium. The ArM0029B mt genome contains a group I intron, with an ORF containing two LAGLIDADG motifs, in cox1. The intronic ORF is shared by C. vulgaris and Prototheca. The phylogeny of the plastid genome reveals that ArM0029B showed a close relationship of Chlorella to Parachlorella and Oocystis within Chlorellales. The distribution of the cox1 intron at 721 support membership in the order Chlorellales. Mitochondrial phylogenomic analyses, however, indicated that ArM0029B shows a greater affinity to MX-AZ01 and Coccomyxa than to the Helicosporidium-Prototheca clade, although the detailed phylogenetic relationships among the three taxa remain to be resolved.ConclusionsThe plastid genome of ArM0029B is similar to that of C. variabilis. The mt sequence of ArM0029B is the first genome to be reported for Chlorella. Chloroplast genome phylogeny supports monophyly of the seven investigated members of Chlorellales. The presence of the cox1 intron at 721 in all four investigated Chlorellales taxa indicates that the cox1 intron had been introduced in early Chorellales as a cis-splice form and that the cis-splicing intron was inherited to recent Chlorellales and was recently trans-spliced in Helicosporidium.