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

2018 ◽  
Vol 23 (7) ◽  
pp. 1313 ◽  
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.

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

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xuelin Wang ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
Suyun Wei ◽  
Xiaogang Dai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Protein Coding ◽  
Ssr Analysis ◽  
Brassicaceae Species ◽  
Mt Genome ◽  
Rna Genes

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.

scholarly journals Complete mitochondrial DNA sequence analysis of Bluespotted seabream, Pagrus caeruleostictus (Perciformes: Sparidae)

2019 ◽  
Author(s):  
Gyamfua Afriyie ◽  
Yusong Guo ◽  
Felix K.A Kuebutornye ◽  
Christian Ayisi Larbi ◽  
Zhongduo Wang
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Molecular Genetic ◽  
Marine Species ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Tropical Regions ◽  
Mitochondrial Dna Sequence ◽  
Rna Genes ◽  
Pagrus Caeruleostictus

Abstract Background Bluespotted seabream, Pagrus caeruleostictus is a benthopelagic marine species found in tropical regions and a member of the family Sparidae and genus Pagrus . In this article, a mitochondrial DNA sequence by high-throughput technique, Illumina Hiseq, was carried out on muscle of the above species and determined the complete mitogenome. Samples were obtained from species collected from the coast of Ghana, West Africa.Results The complete mitochondrial DNA sequence was 16,653 bases pairs in length (GenBank Accession number: MN319701) and comprises of 37 genes; 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a control region as in a typical vertebrate mitochondrial DNA gene. The phylogenetic analysis showed P. caeruleostictus clustered with the clade of P. auriga. Conclusion This research will serve as the foundation for molecular genetic studies of Ghanaian fish species. Moreover, it will contribute to the phylogenetics of class Actinopterygii, order Spariformes, family Sparidae and genus Pagrus.

Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽  
2020 ◽  
Vol 147 (10) ◽  
pp. 1149-1157 ◽  
Author(s):  
Nehaz Muhammad ◽  
Suleman ◽  
Munawar Saleem Ahmad ◽  
Liang Li ◽  
Qing Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Methods ◽  
Sister Relationship ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Relationship Of ◽  
First Time ◽  
Mt Genome ◽  
Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

scholarly journals Analyzing and characterization of the chloroplast genome of Salix suchowensis

2016 ◽  
Author(s):  
Congrui Sun ◽  
Jie Li ◽  
Xiaogang Dai ◽  
Yingnan Chen
Keyword(s):  
Tandem Repeats ◽  
Gene Annotation ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

scholarly journals Genome sequence of Dichelobacter nodosus JKS-07B isolate from J&K, India associated with virulent footrot of sheep

2021 ◽  
Vol 104 (4) ◽  
pp. 003685042110576
Author(s):  
Sabia Qureshi ◽  
Shakil A Wani ◽  
Shaheen Farooq ◽  
Zahid Kashoo ◽  
Basharat Bhat ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Gc Content ◽  
Economic Losses ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Growth And Survival ◽  
Dichelobacter Nodosus ◽  
New Genes ◽  
Potential Vaccine ◽  
Efficacious Vaccine

Introduction: Virulent footrot of sheep caused by Dichelobacter nodosus is associated with tremendous economic losses due to recurrent treatment costs and increased culling rates. This organism being a fastidious anaerobe is difficult to isolate on ordinary media that does not support its growth. The D. nodosus serogroup B isolate described in the present study has been used in the preparation of the whole-cell killed vaccine against footrot in India. D. nodosus serogroup B is the predominant serogroup involved in virulent footrot (lesion score 4) in India as well as in many sheep-rearing countries of the globe. Methods: Genomic DNA was extracted using wizard Genomic DNA purification kit. The whole genome of the D. nodosus strain B was sequenced using an Illumina HiSeq 2500 platform and annotated according to functional gene categories. Annotations were performed using in-house developed Perl scripts using Nr/Nt database, uniprot, Pfam, KEGG, Panther DB, and GO database. Result: The assembled genome size is 1.311,533 Mb and GC content is 44.38. A total of 1215 protein-coding genes, 44tRNA and 7 rRNA were identified. The genome shows 98.63% sequence homology with the reference genome. However, 21 new genes have been identified in this genome. The information will provide insights into the various genes and regulators necessary for D. nodosus growth and survival. Discussion: The genome information of this serogroup B of D. nodosus isolate involved in 85–90% cases of virulent footrot of sheep in India provides further insights for improvement of the killed vaccine (B serogroup) developed recently in India. For the development of an efficacious vaccine against virulent footrot, it is essential to know the serological diversity as well as the virulent status of the strains of the D. nodosus. This serogroup isolate is a potential vaccine candidate to mitigate ovine footrot in India as the majority of virulent footrot cases belong to serogroup B of D. nodosus.

scholarly journals Complete Genome Sequence of Enterobacter roggenkampii Strain KQ-01, Isolated from Bacterial Wilt-Resistant Mulberry Cultivar YS283

Plant Disease ◽  
2021 ◽  
pp. PDIS-07-20-1468
Author(s):  
Yinan Zhou ◽  
Hongyu Yang ◽  
Jiping Liu
Keyword(s):  
Ribosomal Rna ◽  
Bacterial Wilt ◽  
Noncoding Rna ◽  
Gc Content ◽  
Wilt Disease ◽  
Circular Chromosome ◽  
Protein Coding ◽  
First Time ◽  
Rna Genes ◽  
Single Circular Chromosome

An Enterobacter roggenkampii strain, named KQ-01, was isolated for the first time from the diseased roots of the bacterial wilt-resistant mulberry (Morus atropurpurea) cultivar YS283 in the western part of Guangxi Zhuang Autonomous Region, China. E. roggenkampii KQ-01 was characterized by a single, circular chromosome of 4,667,006 bp in size, with a 56.16% GC content. In total, 4,396 genes were annotated, of which 4,281 were assigned as protein-coding genes. In addition, 25 ribosomal RNA, 84 transfer RNA, and 6 noncoding RNA genes as well as 34 pseudogenes were predicted. The resource herein presented will help to explore the pathogenetic mechanisms of mulberry wilt disease caused by genus Enterobacter.

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

Genes ◽  
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.

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

2018 ◽  
Vol 93 (3) ◽  
pp. 383-388 ◽  
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.

scholarly journals Draft Genome Sequence of Lactobacillus plantarum EBKLp545, Isolated from Piglet Feces

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Sukjung Choi ◽  
Eun Bae Kim
Keyword(s):  
South Korea ◽  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Noncoding Rna ◽  
Draft Genome ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Rna Genes

Lactobacillus plantarum strain EBKLp545 was isolated from piglet feces in South Korea and sequenced using an Illumina HiSeq system. This draft genome of strain EBKLp545 consists of 3,306,513 bp with 3,049 protein-coding genes in 138 contigs (≥500 bp), 54 noncoding RNA genes, and a 44.3% G+C content.

scholarly journals Whole-Genome Sequence of Mycobacterium ulcerans CSURP7741, a French Guianan Clinical Isolate

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Jamal Saad ◽  
Marine Combe ◽  
Nassim Hammoudi ◽  
Pierre Couppié ◽  
Romain Blaizot ◽  
...  
Keyword(s):  
Clinical Isolate ◽  
Genome Sequence ◽  
Buruli Ulcer ◽  
Gc Content ◽  
Mycobacterium Ulcerans ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Content Type ◽  
Rna Genes

Combined Nanopore and Illumina whole-genome sequencing of a French Guianan Mycobacterium ulcerans (Buruli ulcer agent) clinical isolate yielded a 5.12-Mbp genome with a 65.5% GC content, 5,215 protein-coding genes, and 51 predicted RNA genes. This publicly available M. ulcerans whole-genome sequence from a strain isolated in South America is closely related to M. ulcerans subsp. liflandii.

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