Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis

Haberlea rhodopensis is a paleolithic tertiary relict species that belongs to the unique group of resurrection plants sharing remarkable tolerance to desiccation. When exposed to severe drought stress, this species shows an ability to maintain structural integrity of its deactivated photosynthetic apparatus, which easily reactivates upon rehydration. In addition to its homoiochlorophyllous nature, the resurrection capability of H. rhodopensis is of particular importance to the global climate change mitigation. In this study, we sequenced, assembled, and analyzed the mitochondrial (mt) genome of H. rhodopensis for the first time. The master circle has a typical circular structure of 484 138 bp in length with a 44.1% GC content in total. The mt genome of H. rhodopensis contains 59 genes in total, including 35 protein-coding, 21 tRNAs, and 3 rRNAs genes. 7 tandem repeats and 85 simple sequence repeats (SSRs) are distributed throughout the mt genome. The alignment of 20 plant mt genomes confirms the phylogenetic position of H. rhodopensis in the Lamiales order. Our comprehensive analysis of the complete mt genome of H. rhodopensis is a significant addition to the limited database of organelle genomes of resurrection species. Comparative and phylogenetic analysis provides valuable information for a better understanding of mitochondrial molecular evolution in plants.

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Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plantSalix suchowensis

PeerJ ◽

10.7717/peerj.3148 ◽

2017 ◽

Vol 5 ◽

pp. e3148 ◽

Cited By ~ 17

Author(s):

Ning Ye ◽

Xuelin Wang ◽

Juan Li ◽

Changwei Bi ◽

Yiqing Xu ◽

...

Keyword(s):

Genome Sequence ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Rrna Genes ◽

Phylogenetic Position ◽

Trna Genes ◽

Shrub Willow ◽

Protein Coding ◽

Protein Coding Genes ◽

Mt Genome

Willow is a widely used dioecious woody plant ofSalicaceaefamily in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence ofS. suchowensiswith the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of theS. suchowensismt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported thatSalixas a sister toPopulus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research ofS. suchowensismt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

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The mitochondrial genome and phylogenetic analysis of the tick Dermacentor everestianus Hirst, 1926 (Acari: Ixodidae)

Systematic and Applied Acarology ◽

10.11158/saa.23.7.8 ◽

2018 ◽

Vol 23 (7) ◽

pp. 1313 ◽

Cited By ~ 2

Author(s):

Zhijun Yu ◽

Shiqi Zhang ◽

Tianhong Wang ◽

Xiaolong Yang ◽

Hui Wang ◽

...

Keyword(s):

Tandem Repeats ◽

Gc Content ◽

Ixodid Tick ◽

Tibet Plateau ◽

Illumina Hiseq ◽

Protein Coding ◽

Illumina Hiseq Sequencing ◽

Dermacentor Everestianus ◽

Mt Genome ◽

Rna Genes

The tick Dermacentor everestianus is widely distributed in Qinghai-Tibet Plateau of China and can transmit many zoonotic pathogens. In the current study, the complete mitochondrial (mt) genome of D. everestianus was sequenced through Illumina HiSeq sequencing. The mt genome is 15,191 bp in length which contains 37 genes, including 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. The overall GC content reached 21.20%, whereas the GC content in the gene region was 21.40%, and in the intergenetic region was 20.50%. Two control regions were sequenced from mt genome of D. everestianus, one located between tRNA-Cys and tRNA-Leu, and the other one was found between rrnS and tRNA-Ile. Two tandem repeats were found between tRNA-Glu and nad1. A phylogenetic tree was constructed based on the complete mitogenome of D. everestianus and 32 other ixodid tick mitogenomes to assess their phylogenetic relationships. D. everestianus is phylogenetically clustered with the tick D. silvarum and D. nuttalli. This is the first complete mt genome of D. everestianus, which provides a useful reference for future studies on systematics and population genetics of this tick species.

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The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea

Zootaxa ◽

10.11646/zootaxa.4243.1.5 ◽

2017 ◽

Vol 4243 (1) ◽

pp. 125 ◽

Cited By ~ 21

Author(s):

YING WANG ◽

JINJUN CAO ◽

WEIHAI LI

Keyword(s):

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Simple Loop ◽

Interspecific Divergence ◽

Family Level ◽

Mt Genome

We present the complete mitochondrial (mt) genome sequence of the stonefly, Styloperla spinicercia Wu, 1935 (Plecoptera: Styloperlidae), the type species of the genus Styloperla and the first complete mt genome for the family Styloperlidae. The genome is circular, 16,129 base pairs long, has an A+T content of 70.7%, and contains 37 genes including the large and small ribosomal RNA (rRNA) subunits, 13 protein coding genes (PCGs), 22 tRNA genes and a large non-coding region (CR). All of the PCGs use the standard initiation codon ATN except ND1 and ND5, which start with TTG and GTG. Twelve of the PCGs stop with conventional terminal codons TAA and TAG, except ND5 which shows an incomplete terminator signal T. All tRNAs have the classic clover-leaf structures with the dihydrouridine (DHU) arm of tRNASer(AGN) forming a simple loop. Secondary structures of the two ribosomal RNAs are presented with reference to previous models. The structural elements and the variable numbers of tandem repeats are described within the control region. Phylogenetic analyses using both Bayesian (BI) and Maximum Likelihood (ML) methods support the previous hypotheses regarding family level relationships within the Pteronarcyoidea. The genetic distance calculated based on 13 PCGs and two rRNAs between Styloperla sp. and S. spinicercia is provided and interspecific divergence is discussed.

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The complete mitochondrial genome of Pseudanoplocephala crawfordi and a comparison with closely related cestode species

Journal of Helminthology ◽

10.1017/s0022149x15000802 ◽

2015 ◽

Vol 90 (5) ◽

pp. 588-595 ◽

Cited By ~ 7

Author(s):

G.H. Zhao ◽

H.B. Wang ◽

Y.Q. Jia ◽

W. Zhao ◽

X.F. Hu ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Taxonomic Status ◽

Amino Acid Sequences ◽

Health Concern ◽

Phylogenetic Position ◽

Protein Coding ◽

Economic Significance ◽

The Family ◽

Mt Genome ◽

Rna Genes

AbstractPseudanoplocephala crawfordi is an important zoonotic cestode of economic significance and public health concern. In spite of its significance as a pathogen, the systematics, genetics, epidemiology and biology of this parasite remain poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of P. crawfordi, which is 14,192 bp long and encodes 36 genes, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. Phylogenetic analysis of the concatenated amino acid sequences using the Bayesian inference (BI) method showed that P. crawfordi was closely related to the family Hymenolepididae. Considering that the taxonomic status of P. crawfordi has been controversial when based only on morphological features, the mt genome obtained here will provide novel molecular markers to ascertain the phylogenetic position of this parasite accurately.

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The complete mitochondrial genome of Pseudopimelodus schultzi Dahl 1955 (Siluriformes, Pseudopimelodidae) and its phylogenetic position within Pseudopimelodidae

Mitochondrial DNA Part B ◽

10.1080/23802359.2021.1945974 ◽

2021 ◽

Vol 6 (8) ◽

pp. 2206-2208

Author(s):

Hanwei Yang ◽

Xiuhui Ma

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Phylogenetic Position

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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