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

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.

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Genome Analyses of a New Mycoplasma Species From the scorpion Centruroides vittatus

10.1101/394825 ◽

2018 ◽

Author(s):

Tsunemi Yamashita ◽

Douglas D. Rhoads ◽

Jeff Pummill

Keyword(s):

Ribosomal Proteins ◽

Gc Content ◽

Fluoroquinolone Resistance ◽

Mycoplasma Species ◽

Virulence Determinants ◽

Circular Chromosome ◽

Protein Coding ◽

Centruroides Vittatus ◽

Genome Analyses ◽

Single Circular Chromosome

ABSTRACTArthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus, and designate it as Mycoplasma vittatus. We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 43.7% and with 1,010 protein-coding genes. The putative virulence determinants include 20 genes associated with the virulence operon associated with protein synthesis (SSU ribosomal proteins) and nine genes with fluoroquinolone resistance. Comparative analysis revealed that the M. vittatus genome is smaller than other Mycoplasma genomes and exhibits a higher GC content. Phylogenetic analysis shows M. vittatus as part of the Hominis group of Mycoplasma. As arthropod genomes accumulate, further novel Mycoplasma genomes may be identified and characterized.

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Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean

Biodiversity Data Journal ◽

10.3897/bdj.9.e72762 ◽

2021 ◽

Vol 9 ◽

Author(s):

Luigi Colin ◽

Chris Yesson ◽

Catherine Head

Keyword(s):

Indian Ocean ◽

Ribosomal Rna ◽

Gc Content ◽

Species Boundaries ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Putative Species ◽

Chagos Archipelago ◽

Rna Genes ◽

Complete Mitochondrial Genomes

We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff. cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.

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Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽

10.3390/genes12081185 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1185

Author(s):

Wenqian Wang ◽

Huan Zhang ◽

Jérôme Constant ◽

Charles R. Bartlett ◽

Daozheng Qin

Keyword(s):

Control Region ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Start Codon ◽

Rrna Genes ◽

Rich Region ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

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The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2004.17.8.827 ◽

2004 ◽

Vol 17 (8) ◽

pp. 827-836 ◽

Cited By ~ 92

Author(s):

Claudia B. Monteiro-Vitorello ◽

Luis E. A. Camargo ◽

Marie A. Van Sluys ◽

João P. Kitajima ◽

Daniela Truffi ◽

...

Keyword(s):

Genome Sequence ◽

Gc Content ◽

Open Reading Frames ◽

Circular Chromosome ◽

Free Sugars ◽

Sugar Transporters ◽

Living Organisms ◽

Bacterial Plant Pathogen ◽

Single Circular Chromosome ◽

Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

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The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific

Parasites & Vectors ◽

10.1186/s13071-019-3711-5 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 4

Author(s):

J. Antonio Baeza ◽

Fabiola A. Sepúlveda ◽

M. Teresa González

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Transfer Rna ◽

The South ◽

Protein Coding ◽

East Pacific ◽

Yellowtail Kingfish ◽

Seriola Lalandi ◽

Rna Genes

Abstract Background The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP). Methods The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens. Results The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species. Conclusions Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.

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

Parasitology ◽

10.1017/s0031182020000906 ◽

2020 ◽

Vol 147 (10) ◽

pp. 1149-1157 ◽

Cited By ~ 1

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).

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The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles

Genes ◽

10.3390/genes11020181 ◽

2020 ◽

Vol 11 (2) ◽

pp. 181

Author(s):

Zhenya Li ◽

Xinxin Li ◽

Nan Song ◽

Huiji Tang ◽

Xinming Yin

Keyword(s):

Ribosomal Rna ◽

Mitochondrial Protein ◽

Carabid Beetles ◽

Protein Coding ◽

Sequencing Method ◽

The Family ◽

Outgroup Species ◽

Complete Mitogenome ◽

Rna Genes ◽

Generation Sequencing

Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.

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The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

Scientific Reports ◽

10.1038/s41598-020-77661-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Wenbin Xu ◽

Boshun Xia ◽

Xinwei Li

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Noncoding Sequences ◽

Chloroplast Genomes ◽

Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

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Characterization of the Complete Mitochondrial Genome of Fischoederius elongatus Derived from Cows in Shanghai, China

BioMed Research International ◽

10.1155/2020/7975948 ◽

2020 ◽

Vol 2020 ◽

pp. 1-6

Author(s):

Zhaoqing Han ◽

Kun Li ◽

Houqiang Luo ◽

Muhammad Shahzad ◽

Khalid Mehmood

Keyword(s):

Amino Acids ◽

Mitochondrial Genome ◽

Ribosomal Rna ◽

Parasite Species ◽

Codon Position ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Protein Coding ◽

Rna Genes

A study was conducted to reveal the characterization of the complete mitochondrial genome of Fischoederius elongatus derived from cows in Shanghai, China. Results indicated that the complete mt genome of F. elongatus was 14,288 bp and contained 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6, and cytb), 22 transfer RNA genes, and two ribosomal RNA genes (l-rRNA and s-rRNA). The overall A + T content of the mt genome was 63.83%, and the nucleotide composition was A (19.83%), C (9.75%), G (26.43%), and T (44.00%). A total of 3284 amino acids were encoded by current F. elongatus isolate mt genome, TTT (Phe) (9.84%) and TTG (Leu) (7.73%) codon were the most frequent amino acids, whereas the ACC (Thr) (0.06%), GCC (Ala) (0.09%), CTC (Leu) (0.09%), and AAC (Asn) (0.09%) codon were the least frequent ones. At the third codon position of F. elongatus mt protein genes, T (50.82%) was observed most frequently and C (5.85%) was the least one. The current results can contribute to epidemiology diagnosis, molecular identification, taxonomy, genetic, and drug development researches about this parasite species in cattle.

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The genome ofHyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C

Archaea ◽

10.1155/2007/745987 ◽

2007 ◽

Vol 2 (2) ◽

pp. 127-135 ◽

Cited By ~ 30

Author(s):

Kim Brügger ◽

Lanming Chen ◽

Markus Stark ◽

Arne Zibat ◽

Peter Redder ◽

...

Keyword(s):

Genome Structure ◽

Trna Genes ◽

Growing Up ◽

Circular Chromosome ◽

Protein Coding ◽

Electron Transfer Proteins ◽

Good Sequence ◽

High Level ◽

Large Clusters ◽

Single Circular Chromosome

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific toH. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Twocdc6genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-typecasgene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

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