scholarly journals The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3692 ◽  
Author(s):  
Fabrizio Ghiselli ◽  
Liliana Milani ◽  
Mariangela Iannello ◽  
Emanuele Procopio ◽  
Peter L. Chang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genetic Variability ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Ruditapes Philippinarum ◽  
Mitochondrial Genomes ◽  
Uniparental Inheritance ◽  
Ruditapes Decussatus ◽  
Important Species ◽  
Two Samples

Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus, also known as the European clam.Ruditapes decussatusis morphologically and ecologically similar to the Manila clamRuditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats ofRuditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembledRuditapes decussatusmitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized theRuditapes decussatusmitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses,Ruditapes decussatusis more genetically similar to species of the Genus Paphia than to the congenericRuditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome ofRuditapes decussatusis a cause or an effect of the ongoing replacement ofRuditapes decussatuswith the invasiveRuditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.

scholarly journals Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

2017 ◽  
Author(s):  
Gisele Lopes Nunes ◽  
Renato Renison Moreira Oliveira ◽  
Eder Soares Pires ◽  
Santelmo Vasconcelos ◽  
Thadeu Pietrobon ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Base Composition ◽  
Iron Ore ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Significant Advance ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rich Region ◽  
The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications

Zootaxa ◽  
2020 ◽  
Vol 4747 (3) ◽  
pp. 547-561
Author(s):  
QING ZHAO ◽  
GERASIMOS CASSIS ◽  
LING ZHAO ◽  
YIFAN HE ◽  
HUFANG ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Stink Bug ◽  
Protein Coding ◽  
Simple Loop ◽  
Phylogenetic Implications ◽  
Maximum Likelihood Methods

Zicrona caerulea (Linnaeus, 1758) is a cosmopolitan stink bug species, which belongs to the predatory subfamily Asopinae. In this study, the complete mitochondrial genome of Zicrona caerulea from Shanxi, China was sequenced for the first time, using next generation sequencing. The mitogenome was found to be 15,479 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 77.14%. All tRNA genes had a clover-leaf structure except for trnS1, which lacks a dihydrouridine (DHU) arm; and for trnV, the DHU arm forms a simple loop. The lengths of rrnS and rrnL were 797 bp and 1,285 bp, respectively. Because of a shortage in tandem repeats, the A+T-rich region was 644 bp in length. Phylogenetic relationships based on these mitogenomes, using Bayesian inference and Maximum likelihood methods, showed that Zicrona caerulea belongs to Asopinae. The monophyly of families of the Pentatomoidea is supported, albeit limited taxon sampling. 

scholarly journals Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Sun ◽  
Hua Huang ◽  
Yudong Liu ◽  
Shanshan Liu ◽  
Jun Xia ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

scholarly journals Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

2018 ◽  
Author(s):  
Ji Haishuo ◽  
Xu Xiaofeng ◽  
Jin Xiufeng ◽  
Cheng Zhi ◽  
jin Hong ◽  
...  
Keyword(s):  
Steady State ◽  
High Resolution ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Transcription Initiation ◽  
Tandem Repeats ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Small Rna Sequencing ◽  
Antisense Gene

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. Most of the new annotations were consistent with the previous annotations which were obtained using PacBio full-length transcripts. Two important findings are that animals transcribe both entire strands of mitochondrial genomes and the tandem repeat in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the H-strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, enriching the fundamental knowledge of mitochondrial biology. This sRNA-seq based method uses 5′ and 3′ end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution and can also be used to identify new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). Animal mitochondrial genomes containing one control region only encode two steady-state lncRNAs, which are the Mitochondrial D-loop 1 (MDL1) and its antisense gene (MDL1AS), while all other reported mitochondrial lncRNAs could be degraded fragments of transient RNAs or random breaks during experimental processing. The high-resolution annotations of mitochondrial genomes can be used to study the phylogenetics and molecular evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics.

scholarly journals Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

2018 ◽  
Author(s):  
Xin-Yan Gao ◽  
Yin-Yin Cai ◽  
Dan-Na Yu ◽  
Kenneth B. Storey ◽  
Jia-Yong Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Nucleotide Composition ◽  
The Other ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Duplicated Genes ◽  
Sister Clade ◽  
Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

scholarly journals Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

2019 ◽  
Author(s):  
Shaun D. Jackman ◽  
Lauren Coombe ◽  
René L. Warren ◽  
Heather Kirk ◽  
Eva Trinh ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Active Sites ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Sitka Spruce ◽  
Physical Structure ◽  
Picea Sitchensis ◽  
Mitochondrial Genomes ◽  
Long Reads ◽  
Branching Points

AbstractPlant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), the largest complete mitochondrial genome of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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