scholarly journals Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)

2019 ◽  
Author(s):  
Rong Zhang ◽  
Jian-Jun Jin ◽  
Michael J. Moore ◽  
Ting-Shuang Yi
Keyword(s):  
Mitochondrial Genome ◽  
Size Structure ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Genes Encoding ◽  
Castanospermum Australe ◽  
A Minor ◽  
High Depth ◽  
Ornamental Species ◽  
Major Conformation

Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inversion were strongly supported. Quantitative assessment of repeat-spanning read pairs showed a major conformation (MC1) and a minor conformation (MC2). The complete mitochondrial genome of C. australe was, thus, generated as 542079bp in length, with a high depth of coverage (~389.7×). Annotation of this mitochondrial genome yielded 58 genes encoding 37 proteins, 18 tRNAs and three rRNAs, as well as 17 introns and three medium-sized repeats (133, 119 and 114bp). Comparison of 10 mitochondrial genomes from Papilionoideae demonstrated significant variation in genome size, structure, gene content and RNA editing sites. In addition, mitochondrial genes were shown to be potentially useful in resolving the deep relationships of Papilionoideae.

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.

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 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.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

2018 ◽  
Author(s):  
Helen. E. Robertson ◽  
Philipp. H. Schiffer ◽  
Maximilian. J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Small Subunit ◽  
Mitochondrial Genomes ◽  
List Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

scholarly journals Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6866 ◽  
Author(s):  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Zhenyi Li ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A New Species ◽  
High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

The mitochondrial genome of the red tomato spider mite, Tetranychus evansi Baker & Pritchard (Acari: Tetranychidae) and its implications for phylogenetic analysis

2019 ◽  
Vol 24 (9) ◽  
pp. 1724-1735
Author(s):  
Jing-Tao Sun ◽  
Jian-Hui Lin ◽  
Qi Zhang ◽  
Dian-Shu Zhao ◽  
Lei Chen ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Spider Mite ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Invasive Pest ◽  
Mitochondrial Genomes ◽  
Illumina Hiseq ◽  
Tetranychus Evansi ◽  
Circular Dna ◽  
Solanaceous Plants

The red tomato spider mite, Tetranychus evansi Baker & Pritchard, is a newly emerged and globally invasive pest of solanaceous plants. In this study, the complete mitochondrial genome of T. evansi was sequenced using Illumina Hiseq technology. The complete mitochondrial genome of T. evansi is a typical circular DNA with a length of 13,064 bp, which contains 37 genes arranged in consistent with the typical metazoan mitochondrial genomes. Highly truncated mitochondrial tRNAs were observed, with 18 of the 22 tRNAs appearing to lack the D- or T- arms or both. A preliminary phylogenic analysis showed that mitochondrial genome can significantly improve the reliability of phylogenetic inference relative to short sequences, as indicated by the elevated bootstrap values. This mitochondrial genome provides a valuable source for the future phylogenetic analyses and helps clear the introduction origins of the Chinese T. evansi populations.

scholarly journals Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae) and evolutionary characteristics

2011 ◽  
Vol 57 (6) ◽  
pp. 785-805 ◽  
Author(s):  
Guiying Chen ◽  
Bin Wang ◽  
Jiongyu Liu ◽  
Feng Xie ◽  
Jianping Jiang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Tandem Duplication ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Tibet Plateau ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding

Abstract The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAMet gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were ((Gymnophiona (Caudata, Anura)). Based on the phylogenetic trees, type 1 was recognized as the ancestral type for amphibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaningful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family.

scholarly journals Comparison of the mitochondrial genomes of the Old and New World strains of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae)

2017 ◽  
Vol 37 (03) ◽  
pp. 125-136
Author(s):  
Tolulope A. Agunbiade ◽  
Brad S. Coates ◽  
Weilin Sun ◽  
Mu-Rou Tsai ◽  
Maria Carmen Valero ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
New World ◽  
De Novo ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Maruca Vitrata ◽  
Mitochondrial Genomes ◽  
Old World ◽  
Pod Borer ◽  
Legume Pod Borer

Abstract Maruca vitrata (Fabricius, 1787) is a cryptic pantropical species of Lepidoptera that are comprised of two unique strains that inhabit the American continents (New World strain) and regions spanning from Africa through to Southeast Asia and Northern Australia (Old World strain). In this study, we de novo assembled the complete mitochondrial genome sequence of the New World legume pod borer, M. vitrata, from shotgun sequence data generated on an Illumina HiSeq 2000. Phylogenomic comparisons were made with other previously published mitochondrial genome sequences from crambid moths, including the Old World strain of M. vitrata. The 15,385 bp M. vitrata (New World) sequence has an 80.7% A+T content and encodes the 13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes in the typical orientation and arrangement of lepidopteran mitochondrial DNAs. Mitochondrial genome-wide comparison between the New and Old World strains of M. vitrata detected 476 polymorphic sites (4.23% nucleotide divergence) with an excess of synonymous substitution as a result of purifying selection. Furthermore, this level of sequence variation suggests that these strains diverged from ~1.83 to 2.12 million years ago, assuming a linear rate of short-term substitution. The de novo assemblies of mitochondrial genomes from next-generation sequencing (NGS) reads provide readily available data for similar comparative studies.

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