Comparison Of Mitochondrial Genomes Research Articles

Mitochondrial Genome Comparison and Phylogenetic Variety of Four Morphologically Similar Bamboo Pests.

Bamboo snout moths (Lepidoptera, Crambidae) comprise the four species: Eumorphobotys obscuralis, Circobotys aurealis, Demobotys pervulgalis, and Crypsiptya coclesalis. These economically important insect pests of bamboo are widely distributed in tropical and subtropical regions. The lack of precise mitochondrial genetic data has impeded the development of effective identification techniques, accurate classification strategies, and targeted prevention and treatment strategies. In this study, we obtained the complete mitochondrial genome sequences of four bamboo snout moth species using high-throughput sequencing. The mitogenomes were 15,103-15,349 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a noncoding region (A + T rich element), consistent with previously studied Crambidae mitogenomes. We reconstructed the phylogenetic relationships among the four species using Bayesian inference and maximum likelihood methods. The moths that fed on bamboo were well clustered in a single clade. Crypsiptya coclesalis was most closely related to D. pervulgalis, while E. obscuralis was most closely related to C. aurealis. The divergence among the main lineages of 97 Lepidoptera species was reconstructed using an uncorrelated relaxed molecular clock. Analyses of the phylogenetic relationships and divergence times showed that the evolution of lepidopteran species has been closely related to that of their hosts. The data support the development of molecular identification techniques for the four species of bamboo snout moth, and our results provide a basis for targeted control strategies.

Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications.

The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from fourCactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations. Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.

Rapid structural evolution of Dendrobium mitogenomes and mito‐nuclear phylogeny discordances in Dendrobium (Orchidaceae)

AbstractReconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next‐generation and third‐generation sequencing technologies. The mitochondrial genomes were 420 538–689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear‐mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single‐copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.

Complete mitochondrial genome sequencing and identification of candidate genes responsible for C5-type cytoplasmic male sterility in cabbage (B. oleracea var. capitata).

Cytoplasmic male sterility (CMS) is widely used in cruciferous vegetables hybrid breeding. The C5-type CMS cabbage line exhibits stable male sterility and offers great value for cabbage breeding. However, the underlying CMS mechanism remains unclear. Here, the complete mitochondrial genome was sequenced and assembled for this line. The genome size was 221,862 bp. Mitochondrial genome comparison showed that the mitochondrial genome was likely generated by recombination with a nap-type CMS B. napus strain. Sixty-seven unknown-function open reading frames (ORFs) were identified. Seven orfs, orf114a, orf123a, orf188a, orf222a, orf261a, orf286a, and orf322a, were specifically identified in this genome. The presence of these candidate CMS genes decreased ATPase activity and ATP content by affecting the transcript levels of energy metabolism-related genes and F1F0-ATP synthase assembly. Among them, orf188a, orf222a, orf261a, orf286a, and orf322a possessed a transmembrane structure, and orf188a was cotranscribed with rps7 and trnfM. orf222a was partially homologous to atp8 and coexpressed with nad5. orf261a and orf322a were cotranscribed with cox1 and atp9, respectively. Additionally, orf114a was cotranscribed with atp8. Yeast two-hybrid assays showed that the ORF222a protein interacts with a B. oleracea ATP17 homolog (Bo7g114140) during F0-type ATP synthase assembly, reducing the quantity and activity of assembled F1F0-ATP synthase. Cytological sections showed that premature separation of the tapetum from the connective tissue and delayed tapetal programmed cell death (PCD) might be the immediate causes of CMS in C5-type CMS cabbage lines. Our results may help uncover the molecular mechanism of C5-type CMS in B. oleracea from the perspectives of the whole mitochondrial genome and cytology of anther development.

Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes in Gossypium hirsutum.

As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton (Gossypium hirsutum), sequencing and de novo assembly were performed on the mitochondrial genome of the G. hirsutum CMS line SI3A, with G. harknessii CMS-D2 cytoplasm, and the corresponding G. hirsutum restorer line 0-613-2R. Remarkable variations in genome structure and gene transcripts were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one. RNA-seq and RT-qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, comparative analysis of RNA-seq and full-length transcripts revealed the complex I gene nad4 to be expressed at a lower level in SI3A than in its restorer and that it featured an intron retention splicing pattern. These two novel chimeric ORFs and nad4 are potential candidates that confer CMS character in SI3A. This study provides new insight into the molecular basis of the nuclear–cytoplasmic interaction mechanism, and that putative CMS genes might be important sources for future precise design cross-breeding of cotton.

Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis

BackgroundMitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.ResultsDraft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondrial DNA contigs were extracted and assembled into complete circular molecules, ranging from 35,104 bp to 49,044 bp in size. All mtDNAs contained the same set of 41 conserved genes with identical gene order. Comparative analyses revealed that introns and intergenic regions were variable, whereas genic regions (including coding sequences, tRNA, and rRNA genes) were conserved. Among 24 introns detected, 11 were in protein-coding genes, 3 in tRNA genes, and the other 10 in rRNA genes. In addition, two mobile fragments were found in intergenic regions. Interestingly, six introns containing N-terminal duplication of the host genes were found in five conserved protein-coding gene sequences. Comparison of genes with and without these introns gave rise to the following proposed model: gene fragment exchange with other species can occur via gain or loss of introns with N-terminal duplication of the host genes.ConclusionsOur findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility.

Genomic differentiation and intercontinental population structure of mosquito vectors Culex pipiens pipiens and Culex pipiens molestus

Understanding the population structure and mechanisms of taxa diversification is important for organisms responsible for the transmission of human diseases. Two vectors of West Nile virus, Culex pipiens pipiens and Cx. p. molestus, exhibit epidemiologically important behavioral and physiological differences, but the whole-genome divergence between them was unexplored. The goal of this study is to better understand the level of genomic differentiation and population structures of Cx. p. pipiens and Cx. p. molestus from different continents. We sequenced and compared the whole genomes of 40 individual mosquitoes from two locations in Eurasia and two in North America. Principal Component, ADMIXTURE, and neighbor joining analyses of the nuclear genomes identified two major intercontinental, monophyletic clusters of Cx. p. pipiens and Cx. p. molestus. The level of genomic differentiation between the subspecies was uniform along chromosomes. The ADMIXTURE analysis determined signatures of admixture in Cx. p. pipens populations but not in Cx. p. molestus populations. Comparison of mitochondrial genomes among the specimens showed a paraphyletic origin of the major haplogroups between the subspecies but a monophyletic structure between the continents. Thus, our study identified that Cx. p. molestus and Cx. p. pipiens represent different evolutionary units with monophyletic origin that have undergone incipient ecological speciation.

Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita

Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1–14000 and Ag0002:50001–61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.

Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes.

Although mitochondrial genomes are typically thought of as single circular molecules, these genomes are fragmented into multiple chromosomes in many eukaryotes, raising intriguing questions about inheritance and (in)stability of mtDNA in such systems. A previous comparison of mitochondrial genomes from two different individuals of the angiosperm species Silene noctiflora found variation in the presence of entire mitochondrial chromosomes. Here, we expand on this work with a geographically diverse sampling of 25 S. noctiflora populations and the closely related species S. turkestanica and S. undulata. Using a combination of deep sequencing and PCR-based screening for the presence of 22 different mitochondrial chromosomes, we found extensive variation in the complement of chromosomes across individuals. Much of this variation could be attributed to recent chromosome loss events, suggesting that the massively expanded and fragmented mitochondrial genomes of S. noctiflora may have entered a phase of genome reduction in which they are losing entire chromosomes at a rapid rate. Sequence analysis of mitochondrial and plastid genomes revealed genealogical differences both between these organelles and within the mitochondrial genome, indicating a history of recombination. Evidence that recombination has generated novel combinations of alleles was more frequent between loci on different mitochondrial chromosomes than it was within chromosomes. Therefore, the fragmentation of mitochondrial genomes and the assortment of chromosomes during mitochondrial inheritance appears to have contributed to a history of sexual-like recombination in the mtDNA of this species.

A comparison of mitochondrial genomes from five species in three genera suggests polyphyly in the subfamily Achatinellinae (Gastropoda: Pulmonata: Stylommatophora: Achatinellidae)

We compare the complete mitochondrial genomes of Achatinella fulgens, A. mustelina, A. sowerbyana, Partulina redfieldi, and Perdicella helena, five species of Hawaiian tree snails across three genera. Mitogenomes ranged in length from 15,187 to 16,793 base pairs, with a base composition of A (36.4–37.4%); T (42.2–42.7%); C (8.8–9.2%); and G (11.3–11.8%). Similar with other pulmonates, these mitogenomes contain 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, with the order conserved among genera. Our study suggests polyphyly in the current arrangement of the subfamily Achatinellinae, part of a spectacular radiation in the Hawaiian Islands.

Intraspecific mitochondrial genome comparison identified CYTB as a high-resolution population marker in a new pest Athetis lepigone

A new outbreak pest, Athetis lepigone (Möschler) (Lepidoptera: Noctuidae), has caused severe economic loss in maize crops in China. In order to conduct population genetics study with a more polymorphic and scientific mitochondrial marker, we sequenced the complete mitochondrial genomes of 13 different A. lepigone individuals. Intraspecific comparison of all PCGs showed that the NADH dehydrogenase and cytochrome b genes had the highest nucleotide diversity. We also found evidence of episodic positive selection on two amino acids, which are encoded by NADH dehydrogenase genes (ND3 and ND4L), against a background of widespread neutral selection of all other mitochondrial PCGs. The genetic divergence observed in this study indicated that the cytochrome b gene (CYTB) is better than COI at recovering population structure. The preliminary population genetic analysis illustrated strong gene flow among A. lepigone populations in China. Our study provides basic information for further research on population genetics of A. lepigone.

Identification of new species of Kalloconus and Africonus (Gastropoda, Conidae) from the Cabo Verde Islands through mitochondrial genome comparison

The new species Kalloconus marimaris sp. nov. and Africonus angeluquei sp. nov. are described from the material obtained during the MNCN sampling campaigns at the Cabo Verde Islands. The new species have been characterized by examination of their shell and radular teeth morphology and by the comparison of mitochondrial genomes obtained through next-generation DNA sequencing techniques. Phylogenetic analyses suggest that K. marimaris sp. nov., known from Sal Island, is a sister species to Kalloconus ateralbus, whereas A. angeluquei sp. nov. from Maio Island is a sister species to Africonus josephinae and Africonus borgesi from Boa Vista Island. The estimated genetic distances were consistent with the full species rank for the new taxa described herein.

The invasion biology of the invasive earwig, Forficula auricularia in Australasian ecosystems

The European earwig, Forficula auricularia, is a cosmopolitan insect endemic to Europe, West Asia and North Africa, which has invaded many temperate regions of the world including Australia and New Zealand. F. auricularia has been shown to be a complex of morphologically identical, reproductively isolated lineages that possess two distinct clades of mitochondrial DNA. Entomological collection data, historical literature and further field collections were used to develop a greater understanding of Australian F. auricularia’s invasion biology and its current distribution. Genetic analysis of F. auricularia collected from Australia and New Zealand using two mitochondrial genes (COI and a fragment overlapping parts of the COI -COII genes) was also undertaken. To identify the possible source populations of the Australasian invasion these sequences were compared to those from 16 locations within Britain and continental Europe. All Australasian populations were shown to be of the clade B lineage. Tasmanian and New Zealand populations consist of a single subclade comprised of only 4 and 1 haplotypes respectively. The Australian mainland populations also contained a second subclade consisting of up to 11 haplotypes indicating that multiple introductions possibly occurred on the Australian mainland. Comparison of mitochondrial genomes from Australasian and European populations showed the Australian mainland subclade to be most closely related to Portuguese haplotypes, and the Tasmanian and New Zealand clade closely related to those in Brittany, France. No European haplotypes perfectly matched the Australasian sequences. Therefore, the original source populations are still to be identified with harbours on the Iberian Peninsula’s western coast and those on the English Channel likely candidate areas.

The Mitochondrial Genome of the Moss Brachythecium rivulare (Hypnales, Brachytheciaceae).

The mitochondrial genome of the pleurocarpous moss Brachythecium rivulare has been sequenced and annotated. The genome consists of 104,460 base pairs and has approximately the same gene set and organization as other bryophyte mitogenomes. Whole mitochondrial genome comparison between B. rivulare and Physcomitrella patens, Tetraphis pellucida, Anomodon rugelii, and Anomodon attenuatus was performed. The primary cause of bryophyte mitochondrial gene length variation was found to be numerous indels in the introns. Bryophyte mitochondrial gene conservation level was estimated, and it was in a good congruence with the overall phylogeny of bryophytes with the percentage of mitogenome similarity being proportional to the age estimated by phylochronologic analysis. Annotation discrepancies in the analyzed mitogenome sequences were identified. The simple sequence repeat (SSR) content was evaluated, and candidate sites of RNA editing were predicted in the B. rivulare mitochondrial genome.

Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema.

BackgroundNematodes belonging to the genus Steinernema are insect parasites and are used as effective biological agents against soil-dwelling insect pests. Although the full nuclear genomes of multiple Steinernema species have become available recently, mitochondrial genome information for the genus is limited. In this study, we sequenced the complete mitochondrial genomes of four species of Steinernema and analysed their structure, codon usage and phylogenetic relationships.ResultsMitochondrial genomes of Steinernema carpocapsae, S. glaseri, S. kushidai and S. litorale comprised 13,924, 13,851, 15,182 and 21,403 bp, respectively, with highly AT-rich nucleotide contents (AT ratio of 71.05–76.76 %). All the expected genes, including 12 protein-coding genes (encoding ATP6, CYTB, COX1-3, ND1-6 and ND4L), two rRNA genes and 22 tRNA genes were identified in the four genomes. Phylogenetic analyses based on the amino acid sequences of the 12 protein-coding genes identified the Steinernema species as monophyletic, representing a sister clade of Rhabditina and Ascaridida. In addition, they were more closely positioned to other Clade 10 nematodes, including Bursaphelenchus xylophilus, Aphelenchoides besseyi and Panagrellus redivivus, than to Strongyloides species. Gene arrangements and codon usage analyses supported this relationship. Mitochondrial genome comparison of two distinct strains of S. carpocapsae detected high intra-specific diversity.ConclusionsThe mitochondrial genomes of four species of Steinernema determined in this study revealed inter- and intra-species divergences/diversities of mitochondrial genomes in this genus. This information provides useful insights into the phylogenetic position of the genus Steinernema within the Nematoda and represents a useful resource for selecting molecular markers for diagnosis and population studies. These data will increase our understanding of the interesting biology of insect parasites.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1730-z) contains supplementary material, which is available to authorized users.

Biohistorical materials and contemporary privacy concerns-the forensic case of King Albert I

The rapid advancement of technology in genomic analysis increasingly allows researchers to study human biohistorical materials. Nevertheless, little attention has been paid to the privacy of the donor’s living relatives and the negative impact they might experience from the (public) availability of genetic results, even in cases of scientific, forensic or historical relevance. This issue has become clear during a cold case investigation of a relic attributed to Belgian King and World War I-hero Albert I who died, according to the official version, in a solo climbing accident in 1934. Authentication of the relic with blood stains assigned to the King and collected on the place where his body was discovered is recognised as one of the final opportunities to test the plausibility of various conspiracy theories on the King’s demise. While the historical value and current technological developments allow the genomic analysis of this relic, publication of genetic data would immediately lead to privacy concerns for living descendants and relatives of the King, including the Belgian and British royal families, even after more than 80 years. Therefore, the authentication study of the relic of King Albert I has been a difficult exercise towards balancing public research interests and privacy interests. The identification of the relic was realised by using a strict genetic genealogical approach including Y-chromosome and mitochondrial genome comparison with living relatives, thereby limiting the analysis to genomic regions relevant for identification. The genetic results combined with all available historical elements concerning the relic, provide strong evidence that King Albert I was indeed the donor of the blood stains, which is in line with the official climbing accident hypothesis and contradicts widespread ‘mise-en-scène’ scenarios. Since publication of the haploid data of the blood stains has the potential to violate the privacy of living relatives, we opted for external and independent reviewing of (the quality of) our data and statistical interpretation by external forensic experts in haploid markers to guarantee the objectivity and scientific accuracy of the identification data analysis as well as the privacy of living descendants and relatives. Although the cold case investigation provided relevant insights into the circumstances surrounding the death of King Albert I, it also revealed the insufficient ethical guidance for current genomic studies of biohistorical material.

Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi

Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.

Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda)

A comparison of mitochondrial genomes of three species of the amphipod Pseudoniphargus revealed the occurrence of a surprisingly high level of gene rearrangement involving protein-coding genes that is a rare phenomenon at low taxonomic levels. The three Pseudoniphargus mitogenomes also display a unique gene arrangement with respect to either the presumed Pancrustacean order or those known for other amphipods. Relative long non-coding sequences appear adjacent to the putative breakage points involved in gene rearrangements of protein coding genes. Other details of the newly obtained mitochondrial genomes – e.g., gene content, nucleotide composition and codon usage – are similar to those found in the mitogenomes of other amphipod species studied. They all contain the typical mitochondrial genome set consisting of 13 protein-coding genes, 22 tRNAs, and two rRNAS, as well as a large control region. The secondary structures and characteristics of tRNA and ribosomal mitochondrial genes of these three species are also discussed.

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.

Sequence and comparison of mitochondrial genomes in the genus Nerita (Gastropoda: Neritimorpha: Neritidae) and phylogenetic considerations among gastropods

In the present study, we determined the mitochondrial DNA (mtDNA) sequence of three Neritas, Nerita versicolor, Nerita tessellata, and Nerita fulgurans. We present an analysis of the features of their gene content and genome organization and compare these within the genus Nerita, and among the main gastropod groups. The new sequences were used in a phylogenetic analysis including all available gastropod mitochondrial genomes. Genomic lengths were quite conserved, being 15,866bp for N. versicolor, 15,741bp for N. tessellata and 15,343bp for N. fulgurans. Intergenic regions were generally short; genes are transcribed from both strands and have a nucleotide composition high in A and T. The high similarity in nucleotide content of the different sequences, gene composition, as well as an identical genomic organization among the Nerita species compared in this study, indicates a high degree of conservation within this diverse genus. Values ​​of Ka/Ks of the 13 protein coding genes (PCGs) of Nerita species ranged from 0 to 0.18, and suggested different selection pressures in gene sequences. Bayesian phylogenetic analyses using concatenated DNA sequences of the 13 PCGs and the two rRNAs, and of amino acid sequences strongly supported Neritimorpha and Vetigastropoda as sister groups.