The Whole Genome Assembly and Comparative Genomic Research ofThellungiella parvula(Extremophile Crucifer) Mitochondrion

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile speciesThellungiella parvula(T. parvula) have been determined with the lengths of 255,773 bp.T. parvulamt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome ofT. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species,T. parvulais related toArabidopsis thalianawhose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

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Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/14/2/9333 ◽

2016 ◽

Vol 14 (2) ◽

pp. 215-224

Author(s):

Lê Thanh Hòa ◽

Nguyễn Thị Khuê ◽

Nguyễn Thị Bích Nga ◽

Đỗ Thị Roan ◽

Đỗ Trung Dũng ◽

...

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Transfer Rna ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Mtdna Sequence ◽

Small Intestinal ◽

Haplorchis Taichui ◽

Rna Genes

The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT) is 15.119 bp in length, containing 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob); 2 ribosomal RNA genes, rrnL (16S) and rrnS (12S); 22 transfer RNA genes (tRNA or trn), and a non-coding region (NR), divided into two sub-regions of short non-coding (short, SNR) and long non-coding (long, LNR). LNR region, 1.692 bp in length, located between the position of trnG (transfer RNA-Glycine) and trnE (Glutamic acid), contains 6 tandem repeats (TR), arranged as TR1A, TR2A, TR1B, TR2B, TR3A, TR3B, respectively. Each protein coding gene (overall, 12 genes), ribosomal rRNA (2 genes) and tRNA (22 genes) were analyzed, in particular, protein-coding genes were defined in length, start and stop codons, and rRNA and tRNA genes for secondary structure.

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

Zootaxa ◽

10.11646/zootaxa.4747.3.8 ◽

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.

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Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

10.21203/rs.3.rs-112827/v1 ◽

2020 ◽

Author(s):

Yan Cheng ◽

Xiaoxue He ◽

S. V. G. N. Priyadarshani ◽

Yu Wang ◽

Li Ye ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Sandy Beaches ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Landscape Plant ◽

Suaeda Glauca ◽

Mt Genome ◽

Mitochondria Genome

Abstract Background Suaeda glauca is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also a beautiful landscape plant with high development prospects and scientific research value. The S. glauca chloroplast genome has recently been reported; however, the mitochondria genome is still unexplored. Results This study assembled the mitochondria genome and annotated the mitochondrial genes of S. glauca based on the Pacbio long reads. The circular mitochondrial genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (27.96%), T (28.01%), C (21.64%), G (21.64%). S. glauca mt genome has 51 genes, including 26 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Phylogenetic analysis with common genes of 28 species resulted in similar morphological classification. Conclusions As a Chenopodiaceae species, S. glauca mt genome will provide insights into the missing pieces in the evolution of sex determination and improve genomic breeding 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 Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

Genes ◽

10.3390/genes10070533 ◽

2019 ◽

Vol 10 (7) ◽

pp. 533

Author(s):

Lei Cui ◽

Rongbo Cao ◽

Yuelei Dong ◽

Xingchen Gao ◽

Jingyi Cen ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Tandem Repeats ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Protein Coding ◽

Conserved Sequence ◽

Complete Mitogenome ◽

First Time ◽

Rna Genes ◽

Complete Mitochondrial Genomes

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

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According to mitochondrial DNA evidence, Parascaris equorum and Parascaris univalens may represent the same species

Journal of Helminthology ◽

10.1017/s0022149x18000330 ◽

2018 ◽

Vol 93 (3) ◽

pp. 383-388 ◽

Cited By ~ 4

Author(s):

J.F. Gao ◽

X.X. Zhang ◽

X.X. Wang ◽

Q. Li ◽

Y. Li ◽

...

Keyword(s):

Severe Illness ◽

Total Amino Acid ◽

Parasitic Infections ◽

Trna Genes ◽

Protein Coding ◽

Parascaris Equorum ◽

Protein Coding Genes ◽

Mt Genome ◽

Rna Genes ◽

Complete Mtdna

AbstractParascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates. The complete mtDNA genome of P. equorum China isolate is 13,899 base pairs (bp), making it the smallest of the four genomes. All four Parascaris mt genomes are circular, and all genes are transcribed in the same direction. The P. equorum mtDNA genome consists of 12 protein-coding genes, two ribosomal RNA genes, 22 transfer (t) RNA genes and one non-coding region, which is consistent with P. equorum Japan isolate and P. univalens Switzerland isolate but distinct from P. univalens USA isolate, which has 20 tRNA genes. Differences in nucleotide sequences of the four entire mt genomes range from 0.1–0.9%, and differences in total amino acid sequences of protein-coding genes are 0.2–2.1%. Phylogenetic analyses showed that the four Parascaris species clustered in a clade, indicating that P. equorum and P. univalens are very closely related. These mt genome datasets provide genetic evidence that P. equorum and P. univalens may represent the same species, which will be of use in further studies of the taxonomy, systematics and population genetics of ascarids and other nematodes.

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The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

10.1101/2022.01.13.476214 ◽

2022 ◽

Author(s):

Shruthy Priya Prakash ◽

Vaidheki Chandrasekar ◽

Selvi Subramanian ◽

Rahamatthunnisha Ummar

Keyword(s):

Mitochondrial Genome ◽

Genome Sequence ◽

Copy Number ◽

Ribosomal Proteins ◽

Tandem Repeats ◽

Sequence Data ◽

Crop Improvement ◽

Whole Genome Sequence ◽

Trna Genes ◽

Mt Genome

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.

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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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Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

Genes ◽

10.3390/genes10090724 ◽

2019 ◽

Vol 10 (9) ◽

pp. 724 ◽

Cited By ~ 1

Author(s):

Xiaolei Yu ◽

Wei Tan ◽

Huanyu Zhang ◽

Weiling Jiang ◽

Han Gao ◽

...

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Ground Beetle ◽

Purifying Selection ◽

Trna Genes ◽

Stem Loop ◽

Protein Coding

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

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