Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons

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.

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.

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Background

The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.

Results

The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmF_C gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.

Conclusions

The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08105-z.

Shifts from cis-to trans-splicing of five mitochondrial introns in Tolypanthus maclurei

Shifts from cis-to trans-splicing of mitochondrial introns tend to correlate with relative genome rearrangement rates during vascular plant evolution, as is particularly apparent in some lineages of gymnosperms. However, although many angiosperms have also relatively high mitogenomic rearrangement rates, very few cis-to trans-splicing shifts except for five trans-spliced introns shared in seed plants have been reported. In this study, we sequenced and characterized the mitogenome of Tolypanthus maclurei, a hemiparasitic plant from the family Loranthaceae (Santalales). The mitogenome was assembled into a circular chromosome of 256,961 bp long, relatively small compared with its relatives from Santalales. It possessed a gene content of typical angiosperm mitogenomes, including 33 protein-coding genes, three rRNA genes and ten tRNA genes. Plastid-derived DNA fragments took up 9.1% of the mitogenome. The mitogenome contained one group I intron (cox1i729) and 23 group II introns. We found shifts from cis-to trans-splicing of five additional introns in its mitogenome, of which two are specific in T. maclurei. Moreover, atp1 is a chimeric gene and phylogenetic analysis indicated that a 356 bp region near the 3′ end of atp1 of T. maclurei was acquired from Lamiales via horizontal gene transfer. Our results suggest that shifts to trans-splicing of mitochondrial introns may not be uncommon among angiosperms.

Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales)

The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.

Horizontal Gene Transfers in Plants

In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.

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.

Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens

Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid ‘ōhi‘a Death (ROD) in Hawai‘i. Despite being sexually incompatible, the two pathogens often co-occur in diseased ‘ōhi‘a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of ‘ōhi‘a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.

Episodic and guanine-cytosine-biased bursts of intragenomic and interspecific synonymous divergence in Ajugoideae (Lamiaceae) mitogenomes

Synonymous substitution rates in plant mitochondrial genomes vary by orders of magnitude among species, whereas synonymous rates among genes within a genome are generally consistent. Exceptionally, genes within the Ajuga reptans (Lamiaceae) mitochondrial genome exhibit unprecedented intragenomic heterogeneity in synonymous sequence divergence, but the biological mechanisms underlying this rate variation remain unclear. We tracked the origin and evolutionary trajectory of mitochondrial rate variations by dense sampling in Ajugoideae and found differences in the timing and magnitude of rate acceleration for particular genes. The most divergent genes accelerated earlier, retained a high rate across Ajugoideae, and are generally devoid of RNA editing, whereas moderately diverged genes accelerated later and retained relatively higher RNA editing frequency. The acceleration of mutation rates correlates with increased guanine-cytosine (GC) content, suggesting a key role for GC-biased gene conversion and/or repair after the breakage of ancestral gene clusters.

Extensive variation in nucleotide substitution rate and gene/intron loss in mitochondrial genomes of Pelargonium

Geraniaceae organelle genomes have been shown to exhibit several highly unusual features compared to most other photosynthetic angiosperms. This includes massively rearranged plastomes with considerable size variation, extensive gene and intron loss, accelerated rates of nucleotide substitutions in both mitogenomes and plastomes, and biparental inheritance and cytonuclear incompatibility of the plastome. Most previous studies have focused on plastome evolution with mitogenome comparisons limited to only a few taxa or genes. In this study, mitogenomes and transcriptomes were examined for 27 species of Geraniales, including 13 species of Pelargonium. Extensive gene and intron losses were detected across the Geraniales with Pelargonium representing the most gene depauperate lineage in the family. Plotting these events on the Geraniaceae phylogenetic tree showed that gene losses occurred multiple times, whereas intron losses more closely reflected the relationships among taxa. In addition, P. australe acquired an intron by horizontal transfer. Comparisons of nucleotide substitution rates in Pelargonium showed that synonymous changes in nuclear genes were much lower than in mitochondrial genes. This is in contrast to the previously published studies that indicated that nuclear genes have 16 fold higher rates than mitochondrial genes across angiosperms. Elevated synonymous substitutions occurred for each mitochondrial gene in Pelargonium with the highest values 783 and 324 times higher than outgroups and other Geraniaceae, respectively. Pelargonium is one of four unrelated genera of angiosperms (Ajuga, Plantago and Silene) that have experienced highly accelerated nucleotide substitutions in mitogenomes. It is distinct from most angiosperms in also having elevated substitution rates in plastid genes but the cause of rate accelerations in Pelargonium plastomes and mitogenomes may be different.

The insertion of a mitochondrial selfish element into the nuclear genome and its consequences

Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double-strand break resulting in the insertion of the HE-encoding gene ("homing" mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and chloroplasts, as well as nuclear ribosomal RNAs. We here report the case of a HE that accidentally integrated into a telomeric region of the nuclear genome of the fungal maize pathogen Ustilago maydis. We show that the gene has a mitochondrial origin, but its original copy is absent from the U. maydis mitochondrial genome, suggesting a subsequent loss or a horizontal transfer from a different species. The telomeric HE underwent mutations in its active site and lost its original start codon. A potential other start codon was retained downstream, but we did not detect any significant transcription of the newly created open reading frame, suggesting that the inserted gene is not functional. Besides, the insertion site is located in a putative RecQ helicase gene, truncating the C-terminal domain of the protein. The truncated helicase is expressed during infection of the host, together with other homologous telomeric helicases. This unusual mutational event altered two genes: The integrated HE gene subsequently lost its homing activity, while its insertion created a truncated version of an existing gene, possibly altering its function. As the insertion is absent in other field isolates, suggesting that it is recent, the U. maydis 521 reference strain offers a snapshot of this singular mutational event.

Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

Variation in protein gene and intron content among land plant mitogenomes

The functional content of the mitochondrial genome (mitogenome) is highly diverse across eukaryotes. Among land plants, our understanding of the variation in mitochondrial gene and intron content is improving from concerted efforts to densely sample mitogenomes from diverse land plants. Here I review the current state of knowledge regarding the diversity in content of protein genes and introns in the mitogenomes of all major land plant lineages. Mitochondrial protein gene content is largely conserved among mosses and liverworts, but it varies substantially among and within other land plant lineages due to convergent losses of genes encoding ribosomal proteins and, to a lesser extent, genes for proteins involved in cytochrome c maturation and oxidative phosphorylation. Mitochondrial intron content is fairly stable within each major land plant lineage, but highly variable among lineages, resulting from occasional gains and many convergent losses over time. Trans-splicing has evolved dozens of times in various vascular plant lineages, particularly those with relatively higher rates of mitogenomic rearrangement. Across eukaryotes, mitochondrial protein gene and intron content has been shaped massive convergent evolution.

A functional twintron, 'zombie' twintrons and a hypermobile group II intron invading itself in plant mitochondria

The occurrence of group II introns in plant mitochondrial genomes is strikingly different between the six major land plant clades, contrasting their highly conserved counterparts in chloroplast DNA. Their present distribution likely reflects numerous ancient intron gains and losses during early plant evolution before the emergence of seed plants. As a novelty for plant organelles, we here report on five cases of twintrons, introns-within-introns, in the mitogenomes of lycophytes and hornworts. An internal group II intron interrupts an intron-borne maturase of an atp9 intron in Lycopodiaceae, whose splicing precedes splicing of the external intron. An invasive, hypermobile group II intron in cox1, has conquered nine further locations including a previously overlooked sdh3 intron and, most surprisingly, also itself. In those cases, splicing of the external introns does not depend on splicing of the internal introns. Similar cases are identified in the mtDNAs of hornworts. Although disrupting a group I intron-encoded protein in one case, we could not detect splicing of the internal group II intron in this ‘mixed’ group I/II twintron. We suggest the name ‘zombie’ twintrons (half-dead, half-alive) for such cases where splicing of external introns does not depend any more on prior splicing of fossilized internal introns.

Horizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits

Horizontal gene transfer (HGT), an important evolutionary mechanism observed in prokaryotes, is the transmission of genetic material across phylogenetically distant species. In recent years, the availability of complete genomes has facilitated the comprehensive analysis of HGT and highlighted its emerging role in the adaptation and evolution of eukaryotes. Endophytes represent an ecologically favored association, which highlights its beneficial attributes to the environment, in agriculture and in healthcare. The HGT phenomenon in endophytes, which features an important biological mechanism for their evolutionary adaptation within the host plant and simultaneously confers "novel traits" to the associated microbes, is not yet completely understood. With a focus on the emerging implications of HGT events in the evolution of biological species, the present review discusses the occurrence of HGT in endophytes and its socio-economic importance in the current perspective. To our knowledge, this review is the first report that provides a comprehensive insight into the impact of HGT in the adaptation and evolution of endophytes.

The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes

Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.

Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum

PREMISE

Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced.

METHODS

By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes.

RESULTS

The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula.

CONCLUSIONS

Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.

The mitochondrial genome of the plant-pathogenic fungus Stemphylium lycopersici uncovers a dynamic structure due to repetitive and mobile elements

Stemphylium lycopersici (Pleosporales) is a plant-pathogenic fungus that has been associated with a broad range of plant-hosts worldwide. It is one of the causative agents of gray leaf spot disease in tomato and pepper. The aim of this work was to characterize the mitochondrial genome of S. lycopersici CIDEFI-216, to use it to trace taxonomic relationships with other fungal taxa and to get insights into the evolutionary history of this phytopathogen. The complete mitochondrial genome was assembled into a circular double-stranded DNA molecule of 75,911 bp that harbors a set of 37 protein-coding genes, 2 rRNA genes (rns and rnl) and 28 tRNA genes, which are transcribed from both sense and antisense strands. Remarkably, its gene repertoire lacks both atp8 and atp9, contains a free-standing gene for the ribosomal protein S3 (rps3) and includes 13 genes with homing endonuclease domains that are mostly located within its 15 group I introns. Strikingly, subunits 1 and 2 of cytochrome oxidase are encoded by a single continuous open reading frame (ORF). A comparative mitogenomic analysis revealed the large extent of structural rearrangements among representatives of Pleosporales, showing the plasticity of their mitochondrial genomes. Finally, an exhaustive phylogenetic analysis of the subphylum Pezizomycotina based on mitochondrial data reconstructed their relationships in concordance with several studies based on nuclear data. This is the first report of a mitochondrial genome belonging to a representative of the family Pleosporaceae.

Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host

Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9-13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.

The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks

The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome. Here we report the sequencing and assembly of the complete mtDNA from the endemic terrestrial Brazilian species Utricularia reniformis. The 857,234bp master circle mitochondrial genome encodes 70 transcriptionaly active genes (42 protein-coding, 25 tRNAs and 3 rRNAs), covering up to 7% of the mtDNA. A ltrA-like protein related to splicing and mobility and a LAGLIDADG homing endonuclease have been identified in intronic regions, suggesting particular mechanisms of genome maintenance. RNA-seq analysis identified properties with putative diverse and important roles in genome regulation and evolution: 1) 672kbp (78%) of the mtDNA is covered by full-length reads; 2) most of the 243kbp intergenic regions exhibit transcripts; and 3) at least 69 novel RNA editing sites in the protein-coding genes. Additional genomic features are hypothetical ORFs (48%), chloroplast insertions, including truncated plastid genes that have been lost from the chloroplast DNA (5%), repeats (5%), relics of transposable elements mostly related to LTR retrotransposons (5%), and truncated mitovirus sequences (0.4%). Phylogenetic analysis based on 32 different Lamiales mitochondrial genomes corroborate that Lentibulariaceae is a monophyletic group. In summary, the U. reniformis mtDNA represents the eighth largest plant mtDNA described to date, shedding light on the genomic trends and evolutionary characteristics and phylogenetic history of the family Lentibulariaceae.

Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding

BACKGROUND

Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns.

RESULTS

For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated.

CONCLUSION

This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.

Mobile Introns Shape the Genetic Diversity of Their Host Genes

Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose nonrandom patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. Through multiple lines of evidence, we rule out relaxed purifying selection as the cause of uneven nucleotide diversity. Instead, our findings implicate intron mobility as a direct driver of host gene diversity. We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or nonrandom patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to empty target sites via homologous recombination. Importantly, however, we show that exonic coconversion can only explain diversity gradients near intron-exon boundaries if the conversion template comes from outside the population. In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations.

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 5.5 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.

Population structure of mitochondrial genomes in Saccharomyces cerevisiae

Background

Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.

Results

To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae.

Conclusions

Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.

Electronic supplementary material

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Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris

Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus.

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.

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty

The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative “parasitism genes.” Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.

Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria

Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome 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.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.

Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns

Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.

The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain

PREMISE OF THE STUDY

The previously sequenced plastome of the hornwort Anthoceros angustus differs from that of other bryophytes by an expanded inverted repeat (IR) and the presence of a type I intron in the 23S ribosomal RNA (rrn23) gene. We assembled the plastome of the hornwort Nothoceros aenigmaticus, contrasted its architecture to that of other bryophytes, and assessed the phylogenetic significance of genomic characters in hornwort evolution. •

METHODS

The Nothoceros plastome was reconstructed from shotgun sequencing of genomic DNA. Comparison with the Anthoceros plastome revealed three structural differences. We sequenced these regions in taxa spanning the hornwort phylogeny. •

KEY RESULTS

The Nothoceros plastome is colinear with other bryophyte plastomes, but differs from the Anthoceros plastome by several gene regions located within the IR in Anthoceros being in the large single-copy region in Nothoceros, by the rrn23 gene lacking an intron, and by the rpl2 being a pseudogene. Comparisons across the hornwort phylogeny indicate that the first two characters are restricted to Anthocerotaceae, while rpl2 pseudogenization diagnoses the sister lineage to Anthocerotaceae. •

CONCLUSIONS

The Nothoceros plastome is structurally similar to that of most bryophytes. However, we identified more structural differences within hornworts than have been described within either the mosses or the liverworts. The distribution of the gene duplication involving the IR and an intron in the rrn23 gene are restricted to Anthocerotaceae. Occurrence of the intron and the conserved intron sequence between Anthoceros and distantly related chlorophyte algae may be due to horizontal gene transfer.

Massive mitochondrial gene transfer in a parasitic flowering plant clade

Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.

Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Here, using phylogenomic approaches, we demonstrate that as much as ∼40% of the mitochondrial genes in the parasitic plant species Rafflesiaceae are acquired from their hosts via HGT. These transgenes are likely functional in their recipient species and in some cases appear to have displaced native copies in the same genomic location. These results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in parasitic plants, HGT involving mitochondrial genes is substantially higher.

Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina

Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.