Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion

Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)

Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.

Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites

BACKGROUND

The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.

SCOPE

This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.

CONCLUSIONS

Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.

Evolution of cox2 introns in angiosperm mitochondria and efficient splicing of an elongated cox2i691 intron

In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. We studied the cox2 from 222 fully-sequenced mitogenomes from 30 angiosperm orders and analyzed the evolution of their introns. Unlike cox2i373, cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 exhibits sporadic elongations, frequently in domain IV of introns. Such elongations are poorly related to repeat content and two of them showed the presence of LINE transposons, suggesting that increasing intron size is very likely due to nuclear intracelular DNA transfer followed by incorporation into the mitochondrial DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases. Although each of the cox2 introns is ∼1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement or the loss of functionality of the interrupted cox2. Through analyzing short-read RNA sequencing of Acacia with a multi-step computational strategy, we found that the Acacia cox2 is functional and its long intron is spliced in cis in a very efficient manner despite its length.

Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences

BACKGROUND

Plant organelle genomes are a valuable resource for evolutionary biology research, yet their genome architectures, evolutionary patterns and environmental adaptations are poorly understood in many lineages. Rhodiola species is a type of flora mainly distributed in highland habitats, with high medicinal value. Here, we assembled the organelle genomes of three Rhodiola species (R. wallichiana, R. crenulata and R. sacra) collected from the Qinghai-Tibet plateau (QTP), and compared their genome structure, gene content, structural rearrangements, sequence transfer and sequence evolution rates.

RESULTS

The results demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes in three Rhodiola species, with the former possessing more conserved genome structure but faster evolutionary rates of sequence, while the latter exhibiting structural diversity but slower rates of sequence evolution. Some lineage-specific features were observed in Rhodiola mitogenomes, including chromosome fission, gene loss and structural rearrangement. Repeat element analysis shows that the repeats occurring between the two chromosomes may mediate the formation of multichromosomal structure in the mitogenomes of Rhodiola, and this multichromosomal structure may have recently formed. The identification of homologous sequences between plastomes and mitogenomes reveals several unidirectional protein-coding gene transfer events from chloroplasts to mitochondria. Moreover, we found that their organelle genomes contained multiple fragments of nuclear transposable elements (TEs) and exhibited different preferences for TEs insertion type. Genome-wide scans of positive selection identified one gene matR from the mitogenome. Since the matR is crucial for plant growth and development, as well as for respiration and stress responses, our findings suggest that matR may participate in the adaptive response of Rhodiola species to environmental stress of QTP.

CONCLUSION

The study analyzed the organelle genomes of three Rhodiola species and demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes. Signals of positive selection were detected in the matR gene of Rhodiola mitogenomes, suggesting the potential role of this gene in Rhodiola adaptation to QTP. Together, the study is expected to enrich the genomic resources and provide valuable insights into the structural dynamics and sequence divergences of Rhodiola species.

Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens

BACKGROUND

Coccidiosis caused by Eimeria is one of the most severe chicken diseases and poses a great economic threat to the poultry industry. Understanding the evolutionary biology of chicken Eimeria parasites underpins development of new interactions toward the improved prevention and control of this poultry disease.

METHODS

We presented an evolutionary blueprint of chicken coccidia by genetically characterizing complete mitogenome assemblies of 33 isolates representing all seven known Eimeria species infecting chickens in China. Further genome- and gene-level phylogenies were also achieved to better understand the evolutionary relationships of these chicken Eimeria at the species level.

RESULTS

33 mitogenomes of chicken eimerian parasites ranged from 6148 bp to 6480 bp in size and encoded typical mitochondrial compositions of apicomplexan parasites including three protein-coding genes (PCGs), seven fragmented small subunit (SSU) and 12/13 fragmented large subunit (LSU) rRNAs. Comparative genomics provided an evolutionary scenario for the genetic diversity of PCGs-cytochrome c oxidase subunits 1 and 3 (cox1 and cox3) and cytochrome b (cytb); all were under purifying selection with cox1 and cox3 being the lowest and highest evolutionary rates, respectively. Genome-wide phylogenies classified the 33 Eimeria isolates into seven subgroups, and furthermore Eimeria tenella and Eimeria necatrix were determined to be more closely related to each other than to the other eight congenic species. Single/concatenated mitochondrial protein gene-based phylogenies supported cox1 as the genetic marker for evolutionary and phylogenetic studies for avain coccidia.

CONCLUSIONS

To our knowledge, these are the first population-level mitogenomic data on the genus Eimeria, and its comprehensive molecular characterization provides valuable resources for systematic, population genetic and evolutionary biological studies of apicomplexan parasites in poultry.

Comparing complete organelle genomes of holoparasitic Christisonia kwangtungensis (Orabanchaceae) with its close relatives: how different are they?

BACKGROUND

Orobanchaceae is the only flowering plant family with species from free-living nonparasite, hemi-parasite to holoparasite, making it an ideal system for studying the evolution of parasitism. However, both plastid and mitochondrial genome have been sequenced in only few parasitic species in Orobanchaceae. Therefore, further comparative study is wanted to investigate the impact of holoparasitism on organelle genomes evolution between close relatives. Here, we sequenced organelle genomes and transcriptome of holoparasitic Christisonia kwangtungensis and compared it with its closely related groups to analyze similarities and differences in adaption strategies to the holoparasitic lifestyle.

RESULTS

The plastid genome of C. kwangtungensis has undergone extensive pseudogenization and gene loss, but its reduction pattern is different from that of Aeginetia indica, the close relative of C. kwangtungensis. Similarly, the gene expression detected in the photosynthetic pathway of these two genera is different. In Orobanchaceae, holoparasites in Buchnereae have more plastid gene loss than Rhinantheae, which reflects their longer history of holoparasitism. Distinct from severe degradation of the plastome, protein-coding genes in the mitochondrial genome of C. kwangtungensis are relatively conserved. Interestingly, besides intracellularly transferred genes which are still retained in its plastid genome, we also found several horizontally transferred genes of plastid origin from diverse donors other than their current hosts in the mitochondrial genome, which probably indicate historical hosts.

CONCLUSION

Even though C. kwangtungensis and A. indica are closely related and share severe degradation of plastome, they adapt organelle genomes to the parasitic lifestyle in different ways. The difference between their gene loss and gene expression shows they ultimately lost photosynthetic genes but through different pathways. Our study exemplifies how parasites part company after achieving holoparasitism.

Horizontal gene transfer in yeasts

Horizontal gene transfer (HGT), defined as the exchange of genetic material other than from parent to progeny, is very common in bacteria and appears to constitute the most important mechanism contributing to enlarge a species gene pool. However, in eukaryotes, HGT is certainly much less common and some early insufficiently consubstantiated cases involving bacterial donors led some to consider that it was unlikely to occur in eukaryotes outside the host/endosymbiont relationship. More recently, plenty of reports of interdomain HGT have seen the light based on the strictest criteria, many concerning filamentous fungi and yeasts. Here, we attempt to summarize the most prominent instances of HGT reported in yeasts as well as what we have been able to learn so far concerning frequency and distribution, mechanisms, barriers, function of horizontally acquired genes, and the role of HGT in domestication.

The complete mitochondrial genome of Mesochaetopterus japonicus (Sedentaria: Chaetopteridae)

The benthic and tube-building polychaete worm Mesochaetopterus japonicus is abundantly present on the coast of the western Pacific. Here, we report the complete mitochondrial genome of M. japonicus, which is 19,326 bp in length and contains 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. All 37 genes are encoded on the heavy strand, and AT content is 70.17%. Phylogenetic analyses based on the M. japonicus mitogenome combined with previously published polychaete mitogenome data revealed that M. japonicus was closely related to Chaetopterus variopedatus and Phyllochaetopterus sp., all of which belong to Chaetopteridae. The mitochondrial genome of M. japonicus could provide useful molecular resources for further research on Polychaeta phylogeny and evolution.

Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.

From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes?

Analysis of genome variation provides insights into mechanisms in genome evolution. This is increasingly appreciated with the rapid growth of genomic data. Mitochondrial genomes (mitogenomes) are well known to vary substantially in many genomic aspects, such as genome size, sequence context, nucleotide base composition and substitution rate. Such substantial variation makes mitogenomes an excellent model system to study the mechanisms dictating mitogenome variation. Recent sequencing efforts have not only covered a rich number of yeast species but also generated genomes from abundant strains within the same species. The rich yeast genomic data have enabled detailed investigation from genome variation into molecular mechanisms in genome evolution. This mini-review highlights some recent progresses in yeast mitogenome studies.

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 complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea

The deep-sea environment is characterized by darkness, hypoxia, and high hydrostatic pressure. Mitochondria play a vital role in energy metabolism; thus, they may endure the selection process during the adaptive evolution of deep-sea organisms. In the present study, the mitogenome of Phymorhynchus sp. from the Haima methane seep was completely assembled and characterized. This mitogenome is 16,681 bp in length and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of most sequenced conoidean gastropods. Some special elements, such as tandem repeat sequences and AT-rich sequences, which are involved in the regulation of the replication and transcription of the mitogenome, were observed in the control region. Phylogenetic analysis revealed that Conoidea is divided into two separate clades with high nodal support. Positive selection analysis revealed evidence of adaptive changes in the mitogenomes of deep-sea conoidean gastropods. Eight residues located in atp6, cox1, cytb, nad1, nad4, and nad5 were determined to have undergone positive selection. This study explores the adaptive evolution of deep-sea conoidean gastropods and provides valuable clues at the mitochondrial level regarding the exceptional adaptive ability of organisms in deep-sea environments.

Horizontal Gene Transfer Involving Chloroplasts

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.

Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant

Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.

Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome

Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.

Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat

Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.

Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts

Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.

The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters

Alicella gigantea (Alicelloidae) is a scavenger with the largest body size among amphipods. It is a participant in the foodweb of deepsea ecosystem and distributed with vast bathymetric and geographic ranges. In this study, the mitochondrial genome of A. gigantea was completely assembled and characterized. The complete sequence has a total length of 16,851 bp, comprising the usual eukaryotic components, with 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 2 noncoding control regions (CRs). The gene rearrangement and reverse nucleotide strand bias of its mitochondrial genome are similar to those observed in the deepsea amphipod Eurythenes maldoror (Eurytheneidae), but different from the characters of Halice sp. MT-2017 (Dexaminoidea), an inhabitant of a deeper environment. Phylogenetic analysis indicates that A. gigantea occupies the basal branch of deepsea species-E. maldoror and Hirondellea gigas. This phylogeny supports the hypothesis that the evolution of hadal amphipods has undergone a transition from the abyssal depth. Compared to 41 available shallow water equivalents, the four accessible mitochondrial genomes from the deep sea, including the one produced in this study, show significantly fewer charged amino acids in the 13 PCGs, which suggests an adaption to the deepsea environment.

Ancient Mitochondrial Gene Transfer between Fungi and the Orchids

The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.

Mitochondria of Cedrus atlantica and allied species: A new chapter in the horizontal gene transfer history

The extraordinary incidence of Horizontal Gene Transfer (HGT) mostly in mitochondrial genomes of flowering plants is well known. Here, we report another episode of HGT affecting a large mitochondrial gene region in the evergreen conifer Atlas cedar (Cedrus atlantica). Mitochondria of this Pinaceae species possess an rps3 gene that harbours two introns and shares the same genomic context with a downstream overlapping rpl16 gene, like in the major groups of gymnosperms and angiosperms analyzed so far. Interestingly, C. atlantica contains additional copies of the rps3 and rpl16 sequences that are more closely related to angiosperm counterparts than to those from gymnosperms, as also confirmed by phylogenetic analyses. This suggests that a lateral transfer from a flowering plant donor is the most likely mechanism for the origin of the Atlas cedar extra sequences. Quantitative PCR and reverse-transcription (RT)-PCR analyses demonstrate, respectively, mitochondrial location and lack of expression for the rps3 and rpl16 additional sequences in C. atlantica. Furthermore, our study provides evidence that a similar HGT event takes place in two other Cedrus species, which occurr in Cyprus and North Africa. Only the West Himalayan C. deodara lacks the transferred genes. The potential donor and the molecular mechanism underlying this lateral DNA transfer remain still unclear.

Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench

Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.

What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts

Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. Historically, mitochondria and plastids were known as "organelles", even before their bacterial origin became fully established. However, since organelle evolution by endosymbiosis has become an established theory in biology, more and more endosymbiotic systems have been discovered that show various levels of host/symbiont integration. In this context, the distinction between "host/symbiont" and "eukaryote/organelle" systems is currently unclear. The criteria that are commonly considered are genetic integration (via gene transfer from the endosymbiont to the nucleus), cellular integration (synchronization of the cell cycles), and metabolic integration (the mutual dependency of the metabolisms). Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. I would like to call this aspect of integration "sexual symbiont integration". If the partners lose their independence in speciation, I think that they should be considered one species. The partner who maintains its genetic recombination mechanisms and life cycle should then be the name giving "host"; the other one would be the organelle. Distinguishing between organelles and symbionts according to their sexual symbiont integration is independent of any particular mechanism or structural property of the endosymbiont/host system under investigation.

Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid-derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.

Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.

Intercompartmental Piecewise Gene Transfer

Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes.

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.

Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer

Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.

Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant

Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT. The sequencing of the complete mtDNA of L. mirabile revealed the unprecedented acquisition of host-derived mitochondrial genes, representing 80% of the protein-coding gene content. All but two of these foreign genes replaced the native homologs and are probably functional in energy metabolism. The genome consists of 54 circular-mapping chromosomes, 25 of which carry no intact genes. The likely functional replacement of up to 26 genes in L. mirabile represents a stunning example of the potential effect of rampant HGT on plant mitochondria. The use of host-derived genes may have a positive effect on the host-parasite relationship, but could also be the result of nonadaptive forces.

Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer

Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes.

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species

Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments.

Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium

The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches.

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis

The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr)-tRNA(Pro) intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY)) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

The Complete Moss Mitochondrial Genome in the Angiosperm Amborella Is a Chimera Derived from Two Moss Whole-Genome Transfers

Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR). These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.

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 5.5 Myr. 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.

Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA

The most gene-rich and bacterial-like mitochondrial genomes known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mitochondrial DNA (mtDNA), including a cox15 gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thus cox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identify A. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of α-proteobacteria (>670 sequences), whereas A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two α-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only is cox15-1 a relatively recent acquisition unique to the Andalucia lineage but also the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all α-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.

The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.

Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast

The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.

Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

PREMISE OF THE STUDY

Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries.

METHODS

Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests.

KEY RESULTS

The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins.

CONCLUSIONS

This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.

Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch)

Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.

Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant

The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants. We conducted the first study in which the organellar genomes of a cybrid - between Nicotiana tabacum and Hyoscyamus niger - were sequenced and compared to those of its parents. This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes. Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double-strand break repair and/or break-induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene - and genome - transfer in angiosperm mitochondrial DNAs.

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.

History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes

Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.

HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion

Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When "duplicative HGT" introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term "HGT turbulence" to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.

Molecular evolution and functional characterisation of an ancient phenylalanine ammonia-lyase gene (NnPAL1) from Nelumbo nucifera: novel insight into the evolution of the PAL family in angiosperms

Background

Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the production of secondary metabolites. This enzyme has been identified in many organisms, ranging from prokaryotes to higher plants. Because Nelumbo nucifera is a basal dicot rich in many secondary metabolites, it is a suitable candidate for research on the phenylpropanoid pathway.

Results

Three PAL members, NnPAL1, NnPAL2 and NnPAL3, have been identified in N. nucifera using genome-wide analysis. NnPAL1 contains two introns; however, both NnPAL2 and NnPAL3 have only one intron. Molecular and evolutionary analysis of NnPAL1 confirms that it is an ancient PAL member of the angiosperms and may have a different origin. However, PAL clusters, except NnPAL1, are monophyletic after the split between dicots and monocots. These observations suggest that duplication events remain an important occurrence in the evolution of the PAL gene family. Molecular assays demonstrate that the mRNA of the NnPAL1 gene is 2343 bp in size and encodes a 717 amino acid polypeptide. The optimal pH and temperature of the recombinant NnPAL1 protein are 9.0 and 55°C, respectively. The NnPAL1 protein retains both PAL and weak TAL catalytic activities with K_m values of 1.07 mM for L-phenylalanine and 3.43 mM for L-tyrosine, respectively. Cis-elements response to environmental stress are identified and confirmed using real-time PCR for treatments with abscisic acid (ABA), indoleacetic acid (IAA), ultraviolet light, Neurospora crassa (fungi) and drought.

Conclusions

We conclude that the angiosperm PAL genes are not derived from a single gene in an ancestral angiosperm genome; therefore, there may be another ancestral duplication and vertical inheritance from the gymnosperms. The different evolutionary histories for PAL genes in angiosperms suggest different mechanisms of functional regulation. The expression patterns of NnPAL1 in response to stress may be necessary for the survival of N. nucifera since the Cretaceous Period. The discovery and characterisation of the ancient NnPAL1 help to elucidate PAL evolution in angiosperms.

Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae)

Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2–rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.