Mitochondrial Genome Size Research Articles

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

BackgroundDalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers.ResultsWe integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome.ConclusionFor the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

The complete mitochondrial genome of Poropanchax normani and phylogenetic studies of Cyprinodontidaes

The complete mitochondrial genome of the Cyprinodontiformes fish Poropanchax normani was studied in this study. The size of the entire mitochondrial genome was 16,878 bp, and the total length of the encoding sequence was 11,435 bp, accounting for 67.75%, encoding 3800 amino acids in total. Genome base compositions were: A was 27.30%, C was 28.30%, G was 16.17%, and T was 28.23%. ND2 and CO1 started with GTG, and other protein-coding genes started with ATG. ND1, ND2, and ND3 ended with TAG, respectively, CO2 and ND4 ended with a single T, and other PCGS ended with TAA. The ribosomal RNA lengths of 12S and 16S were 950 bp and 1690 bp, respectively. The control area (D-loop) was 1194 bp in size and ranged from 15,685 to 16,878 bp. It showed negative GC skew value (–0.2728) and negative AT skewness (–0.0168). Phylogenetic analysis showed that P. normani was most closely related to Xenotoca eiseni. The complete sequence of the mitochondrial genome will provide a new perspective for classification and help to draw a more complete picture of species diversity within the Cyprinodontiformes.

Another polymorphic mitochondrial genome of Grampus griseus and phylogeny of family Delphinidae

Risso’s dolphin (Grampus griseus Cuvier, 1812) is the only species of genus Grampus and a cosmopolitan marine inhabitant. Here, we report a polymorphic complete mitochondrial genome of G. griseus. The size of the total mitochondrial genome was 16,386 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. 37 single nucleotide polymorphic sites (SNPs) were identified compared to the references. Based on the available total mitochondrial dolphin genomes’ phylogenetics, G. griseus has formed a clade with 0.1415 distance, sister to the following species of the subfamily Globicephalinae and the taxonomy of Orcinus orca still needs further investigations.

The complete mitochondrial genome of Trematomus loennbergii (Perciformes, Nototheniidae)

The complete mitochondrial genome of Trematomus loennbergii was studied using NGS technology with PacBio platform. The mitochondrial genome size was 19,374bp and it had 13 protein-coding genes, 22 tRNAs and 2 rRNAs. There were 4 types of stop codons which were TAA, TAG, AGG and T(AA) but start codon type was only one (ATG). The contents of GC were 44.09% and AT contents were 55.91%. To conduct phylogenetic analysis, 12 species in 3 families were used. The result suggested that T. loennbergii was close to Pagothenia borchgrevinki in Nototheniidae. This study would provide a fundamental data for molecular evolution of T. loennbergii.

Complete mitochondrial genome of the copepod Sinergasilus undulates (Copepoda: Poecilostomatoida)

The total mitochondrial genome size of Sinergasilus undulatus is 14,239 bp in length, including 13 protein-coding genes (PCGs), two rRNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop). The overall nucleotide composition of the mitochondrial DNA of S. undulatus is 34.9% A, 35.5% T, 15.7% C, 13.9% G, and 70.4% AT, respectively. Phylogenetic analysis suggests that the genus Sinergasilus is monophyletic, and S. undulatus is closely related to S. polycolpus. The complete mitochondrial genome of S. undulatus would be useful for species identification, epidemiology, and phylogenetics among Copepods.

Panorama of intron dynamics and gene rearrangements in the phylum Basidiomycota as revealed by the complete mitochondrial genome of Turbinellus floccosus.

In the present study, the complete mitogenome of Turbinellus floccosus was sequenced, assembled, and compared with other basidiomycete mitogenomes. The mitogenome of T. floccosus consists of a circular DNA molecule, with a size of 62,846 bp. Gene arrangement analysis indicated that large-scale gene rearrangements occurred in the levels of family and genus of basidiomycete species, and the mitogenome of T. floccosus contained a unique gene order. A significant correlation between the number of introns and the mitochondrial genome size of Basidiomycota were detected (P < 0.01). A total of 896 introns were detected in the core protein-coding genes (PCGs) of 74 basidiomycete species, and the cox1 gene was the largest host gene of basidiomycete introns. Intron position class (Pcls) P383 in the cox1 gene was the most common intron in Basidiomycota, which distributed in 40 of 74 basidiomycete species. In addition, frequent intron loss/gain events were detected in basidiomycete species. More than 50% of bases around insertion sites (- 15 bp to 15 bp) of Pcls from different species were conservative, indicating site preferences of intron insertions in Basidiomycota. Further analysis showed that 76.09% of introns tended to insert downstream to a T base in Basidiomycota. Phylogenetic analysis for 74 basidiomycetes indicated mitochondrial genes are effective molecular markers for phylogeny of basidiomycetes. The study served as the first report on the mitogenome from the family Gomphaceae, which will help to understand the intron origin and evolution in Basidiomycota. KEY POINTS: • The mitogenome of Turbinellus floccosus had a unique gene arrangement. • Intron loss/gain events were detected in the 74 basidiomycete species. • Introns tend to insert downstream of a T base in basidiomycete mitogenomes.

Utility of the Mitochondrial Genome in Plant Taxonomic Studies.

Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.

The complete mitochondrial DNA sequence of Heterochaerus australis (Acoela, Convolutidae)

One complete mitochondrial genomes (mitogenomes) was determined for Heterochaerus australis (Acoela, Convolutidae). Its mitochondrial genome size was 13,885 bp. The sequence contains 2 ribosomal RNA genes (rrnL and rrnS), 20 tRNA genes, and 12 protein-coding genes (PCGs). The A + T content of the complete mitochondrial genome sequence was 70.8%. The base composition showed a tendency of high AT. The resulted maximum likelihood (ML) tree supported that Acoela had a distant relationship with other orders of Turbellaria and the Xenacoelomorpha.

Complete sequence of mitochondrial DNA of a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae)

One complete mitochondrial genome (mitogenome) was determined for a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). The mitochondrial genome size of the sea cucumber was 15,920 bp. The sequence contains 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of AT. The resulted maximum likelihood (ML) tree of Holothuroidea supported that Synallactes sp. is a species of Synallactida.

Complete mitochondrial genome sequences of sea slug Melanochlamys sp. (Cephalaspidae: Aglajidae)

One complete mitochondrial genome (mitogenomes) was determined for Melanochlamys sp. (Cephalaspidae: Aglajidae). The mitochondrial genome size was 13,795 bp. The sequence contains two ribosomal RNA genes (rrnL and rrnS), 20 tRNA genes, and 12 protein-coding genes (PCGs). The A + T content of the complete mitochondrial genome sequence was 68.2%. The base composition showed a tendency of high AT. The resulted maximum-likelihood (ML) tree of Opisthobranchia supported that genetic differences between Melanochlamys sp. with other species of Cephalaspidae, so that there is a well-defined separation of clades.

The mitogenome of Pseudocrossidium replicatum, a desiccation-tolerant moss

Bryophytes are the earliest plant group on Earth. They are a fundamental component of many ecosystems around the World. Some of their main roles are related to soil development, water retention, and biogeochemical cycling. Bryophytes include liverworts, hornworts, and mosses. The sequencing of chloroplast and mitochondria genomes has been useful to elucidate the taxonomy of this heterogeneous plant group. To date, despite their ecological importance only 41 mosses mitogenomes have been deposited in the GenBank. Here, the complete mitochondria genome sequence of Pseudocrossidium replicatum, a moss of the Pottiaceae family isolated in Tlaxcala, Mexico, is reported. The mitochondrial genome size of P. replicatum comprises 105,495 bp and contains the groups of genes described for other bryophytes mitogenomes. Our phylogenetic analysis shows that during the evolution of the mosses’ mitogenome, nad7, rps4, rpl16, and rpl10 genes were lost independently in several lineages. The complete mitogenome sequence reported here would be a useful tool for our comprehension of the evolutionary and population genetics of this group of plants.

Complete mitochondrial DNA of the marine water flea Diaphanosoma celebensis (Cladocera, Sididae)

The complete mitochondrial genome was sequenced from the marine water flea Diaphanosoma celebensis. The sequenced mitochondrial genome size was 17,060 bp, possessing identical gene order of 13 protein-coding genes (PGCs) to those of the congeneric freshwater species Diaphanosoma dubium in the genus Diaphanosoma. The mitochondrial genome of D. celebensis had 13 PGCs, two rRNAs, and 22 tRNAs. Of 13 PGCs, three genes (CO3, ND3, and ND4) had incomplete stop codons. Furthermore, the stop codons of the remaining ten PGCs were TAA (for CO1, ATP8, ATP6, ND5, ND6, and ND1) and TAG (for NL4L, Cytb, and ND2). The second and third base composition of codon on 9 PCGs on the L strand in D. celebensis mitogenome showed an anti-G bias (11.0% and 15.0%), respectively.

Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size

Arcoida, comprising about 570 species of blood cockles, is an ecologically and economically important lineage of bivalve molluscs. Current classification of arcoids is largely based on morphology, which shows widespread homoplasy. Despite two recent studies employing multi-locus analyses with broad sampling of Arcoida, evolutionary relationships among major lineages remain controversial. Interestingly, mitochondrial genomes of several ark shell species are 2–3 times larger than those found in most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. These results highlight the need of detailed phylogenetic study to explore evolutionary relationships within Arcoida so that the evolution of mitochondrial genome size can be understood. To this end, we sequenced 17 mitochondrial genomes and compared them with publicly available data, including those from other lineages of Arcoida with emphasis on the subclade Arcoidea species. Our phylogenetic analyses indicate that Noetiidae, Cucullaeidae and Glycymerididae are nested within a polyphyletic Arcidae. Moreover, we find multiple independent expansions and potential contractions of mitochondrial genome size, suggesting that the large mitochondrial genome is not a shared ancestral feature in Arcoida. We also examined tandem repeats and inverted repeats in non-coding regions and investigated the presence of such repeats with relation to genome size variation. Our results suggest that tandem repeats might facilitate intraspecific mitochondrial genome size variation, and that inverted repeats, which could be derived from transposons, might be responsible for mitochondrial genome expansions and contractions. We show that mitochondrial genome size in Arcoida is more dynamic than previously understood and provide insights into evolution of mitochondrial genome size variation in metazoans.

Complete mitochondrial genome of the freshwater water flea Daphnia magna NIES strain (Cladocera, Daphniidae): Rearrangement of two ribosomal RNA genes

The complete mitochondrial genome was sequenced from the NIES strain of the freshwater water flea Daphnia magna. The sequenced mitochondrial genome size of the NIES strain of D. magna was 17,432 bp, possessing identical gene order and the contents to those of the congeneric species Daphnia galeata in the genus Daphnia, but 16S and 12S rRNA genes was in opposite direction compared to other daphnid, while ND2 gene was also often found in opposite direction in the genus Daphnia. Overall, the mitochondrial genome of D. magna NIES strain has 13 protein-coding genes (PGCs), two rRNAs, and 22 tRNAs. Of 13 PGCs, four genes (CO1, CO2, ND5, and ND4) had incomplete stop codons. Furthermore, the stop codons of the remaining nine PGCs were TAG and TAA, while the start codons of CO1, ND6, and ND3 genes were ATT, ATT, and ATC, respectively. The base composition of D. magna NIES strain mitogenome shows an anti-G and –T bias (16.5% and 16.0%) on the L strand, respectively.

Integrative Systematic Revision of Bolitoglossa celaque (Caudata: Plethodontidae), with a new species from the Lenca Highlands of Honduras

The diversity of the tropical climbing salamander genus Bolitoglossa (Magnadigita) in Honduras has been underestimated historically, with 11 new species having been described in the past quarter-century. Bolitoglossa celaque is known to occur in three disjunct mountain ranges across the Lenca Highlands region of southwestern Honduras, and previous studies have independently demonstrated differences in mitochondrial genealogy and genome size between populations to the east and west of the Mejocote–San Juan Depression. Sampling from all three mountain ranges represented two genetically distinct clades: one associated with the vicinity of the type locality, Montana de Celaque, and the second consisting of several eastern populations from the departments of Intibuca and La Paz. Distinctiveness of these two clades was further investigated and supported by analyses of morphological variation, geometric morphometrics of foot morphology, and comparative osteology. Based on congruent signals from each line of evidence, we restrict the taxon B. celaque to Montana de Celaque and describe the eastern populations as a new species of Bolitoglossa.

Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent

BackgroundOrganelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).ResultsPhylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae).ConclusionThis study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.

Three complete mitochondrial genomes of freshwater fishes in the genus Abbottina (Cypriniformes: Gobionidae)

Abbottina binhi has been misidentified as Abbottina rivularis in China for a long time. In this study, we determined three mitochondrial genomes of A. rivularis and A. binhi such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7–56.5% in the base compositions. Our reconstructed phylogeny showed that A. rivularis and A. binhi formed a sister taxon relationship, and they together were a monophyletic group.

The complete mitochondrial genomes of Aporia crataegi, Gonepteryx rhamni, and Appias remedios (Lepidoptera, Pieridae) and phylogenetic relationship of other Pieridae species.

Pieridae is a butterfly family whose higher classification has not yet been settled. In this research, we used completed mitochondrial genome sequence to identify and analyze the relationship of three subfamilies of Pieridae (Dismorphiinae, Coliadinae and Pierinae). We have sequenced the complete mitogenomes of Aporia crataegi, Gonepteryx rhamni, and Appias remedios, which are 15,148 bp, 15,118 bp and 15,223 bp in length, respectively. These three mitogenomes have a typical set of 37 genes and an A+T-rich region. The protein-coding genes, excluding the cox1 gene, in the three mitogenomes are initiated by the typical ATN codons. The putative initiation codon for the cox1 gene in the three species is CGA. tRNA genes in the three Pieridae mitogenomes show typical clover leaf structures, except tRNASer(AGN) which lacks the dihydrouridine (DHU) stem. The length of A+T-rich region varies in the three species, which leads to the variation in the mitochondrial genome size. The characterizations of the three mitogenomes enrich our knowledge on the Lepidopteran mitogenome and provide us genetic information to reconstruct the phylogenetic tree. Finally, the phylogenetic analyses using mitogenome data showed that the relationship among three subfamilies of Pieridae is (Dismorphiinae + (Coliadinae + Pierinae)).

The complete mitochondrial genome sequence of cabbage looper, Trichoplusia ni (Lepidoptera: Noctuidae)

Trichoplusia ni is a polyphagous insect that feeds on many crops plants of economic importance. In this paper, we presented the complete mitochondrial genome of T. ni. The circular mitochondrial genome size is 15,239 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), two ribosome RNA genes (rRNA), and a control region of 1103 bp in length. The base composition of the genome is as follows: A of 38.9%, T of 41.6%, C of 11.5%, and G of 8.0%, with a total G + C content of the mitochondrial genome 19.5% and A + T of 80.5%. The phylogenetic Neighbour-Joining (NJ) tree was constructed to validate the taxonomic status of T. ni, exhibiting a closest relationship with Spodoptera litura and Spodoptera frugiperda. The research of the complete mitochondrial genome of Trichoplusia ni is able to provide a reference taxonomic relationships and more data of the insect for further.