Gene Order Arrangement Research Articles

Complete mitochondrial genome of a brown frog, Rana kunyuensis (Anura: Ranidae)

The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNALeu(CUN) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.

Complete mitochondrial genome of a freshwater snail, Semisulcospira libertina (Cerithioidea: Semisulcospiridae)

The first complete mitochondrial genome (mitogenome) of Cerithioidea (Gastropoda: Caenogastropoda) was determined using a freshwater snail Semisulcospira libertina (Cerithioidea: Semisulcospiridae) as a representative species of the superfamily. The mitogenome was 15,432 bp in length, including 13 typical invertebrate protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition was 31.4% for A, 17.8% for C, 34.8% for T and 16.0% for G with a A + T bias. The mitogenome of S. libertina displayed novel gene order arrangement compared with published Caenogastropoda mitogenomes to date. This mitogenome contributed in resolving phylogenetic position and interrelationships of Cerithioidea.

Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

BackgroundAlthough it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline.ResultsThe complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax.ConclusionsWe infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry.The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969–18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1–6, nad4L, cox1–3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.

The complete mitochondrial genome of the large white-bellied rat, Niviventer excelsior (Rodentia: Muridae)

The first complete mitochondrial genome of the large white-bellied rat (Niviventer excelsior) was sequenced and annotated in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The mitochondrial genome sequence (16,298 bp) of N. excelsior contains 13 protein-coding, 2 rRNA and 22 tRNA genes as well as 1 typical control region (D-Loop), which are shared by other mammalian mitochondrial genomes. The codon usage also followed the typical vertebrate pattern except for an unusual CCA stop codon, which was termination codon of Cyt b. The 16 nucleotide insertion was detected in the central conserved domain of d-Loop. The 12 heavy-strand encoded protein-coding genes were used to reconstruct the phylogenetic relationships by the Bayesian inference and maximum likelihood methods. Topologies revealed that N. excelsior clustered together with the species in genus Rattus, indicating their closer phylogenetic relationship.

Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs.

BackgroundWidespread sampling of vertebrates, which comprise the majority of published animal mitochondrial genomes, has led to the view that mitochondrial gene rearrangements are relatively rare, and that gene orders are typically stable across major taxonomic groups. In contrast, more limited sampling within the Phylum Mollusca has revealed an unusually high number of gene order arrangements. Here we provide evidence that the lability of the molluscan mitochondrial genome extends to the family level by describing extensive gene order changes that have occurred within the Vermetidae, a family of sessile marine gastropods that radiated from a basal caenogastropod stock during the Cenozoic Era.ResultsMajor mitochondrial gene rearrangements have occurred within this family at a scale unexpected for such an evolutionarily young group and unprecedented for any caenogastropod examined to date. We determined the complete mitochondrial genomes of four species (Dendropoma maximum, D. gregarium, Eualetes tulipa, and Thylacodes squamigerus) and the partial mitochondrial genomes of two others (Vermetus erectus and Thylaeodus sp.). Each of the six vermetid gastropods assayed possessed a unique gene order. In addition to the typical mitochondrial genome complement of 37 genes, additional tRNA genes were evident in D. gregarium (trnK) and Thylacodes squamigerus (trnV, trnLUUR). Three pseudogenes and additional tRNAs found within the genome of Thylacodes squamigerus provide evidence of a past duplication event in this taxon. Likewise, high sequence similarities between isoaccepting leucine tRNAs in Thylacodes, Eualetes, and Thylaeodus suggest that tRNA remolding has been rife within this family. While vermetids exhibit gene arrangements diagnostic of this family, they also share arrangements with littorinimorph caenogastropods, with which they have been linked based on sperm morphology and primary sequence-based phylogenies.ConclusionsWe have uncovered major changes in gene order within a family of caenogastropod molluscs that are indicative of a highly dynamic mitochondrial genome. Studies of mitochondrial genomes at such low taxonomic levels should help to illuminate the dynamics of gene order change, since the telltale vestiges of gene duplication, translocation, and remolding have not yet been erased entirely. Likewise, gene order characters may improve phylogenetic hypotheses at finer taxonomic levels than once anticipated and aid in investigating the conditions under which sequence-based phylogenies lack resolution or prove misleading.

The mitochondrial genome of Priapulus caudatus Lamarck (Priapulida: Priapulidae)

We sequenced and annotated the complete mitochondrial (mt) genome of the priapulid Priapulus caudatus in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The genome was 14,919 bp in its entirety with few, short non-coding regions. A number of protein-coding and tRNA genes overlapped, making the genome relatively compact. The gene order was: cox1, cox2, trnK, trnD, atp8, atp6, cox3, trnG, nad3, trnA, trnR, trnN, rrnS, trnV, rrnL, trnL(yaa), trnL(nag), nad1, − trnS(nga), − cob, − nad6, trnP, − trnT, nad4L, nad4, trnH, nad5, trnF, − trnE, − trnS(nct), trnI, − trnQ, trnM, nad2, trnW, − trnC, − trnY; where ‘−’ indicates genes transcribed on the opposite strand. The gene order, although unique amongst Metazoa, shared the greatest number of gene boundaries and the longest contiguous fragments with the chelicerate Limulus polyphemus. The mt genomes of these taxa differed only by a single inversion of 18 contiguous genes bounded by rrnS and trnS(nct). Other arthropods and nematodes shared fewer gene boundaries but considerably more than the most similar non-ecdysozoan.

Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi.

The extent to which the order of genes along chromosomes is conserved between Saccharomyces cerevisiae and related species was studied by analysing data from DNA sequence database. As expected, the extent of gene order conservation decreases with increasing evolutionary distance. About 59% of adjacent gene pairs in Kluyveromyces lactis or K. marxianus are also adjacent in S. cerevisiae, and a further 16% of Kluyveromyces neighbours can be explained in terms of the inferred ancestral gene order in Saccharomyces prior to the occurrence of an ancient whole-genome duplication. Only 13% of Candida albicans linkages, and no Schizosaccharomyces pombe linkages, are conserved. Analysis of gene order arrangements, chromosome numbers, and ribosomal RNA sequences suggests that genome duplication occurred before the divergence of the four species in Saccharomyces sensu stricto (all of which have 16 chromosomes), but after this lineage had diverged from Saccharomyces kluyveri and the Kluyveromyces lactislmarxianus species assemblage.