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1.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(6): 3985-3986, 2016 11.
Article in English | MEDLINE | ID: mdl-25543913

ABSTRACT

The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.


Subject(s)
Decapoda/genetics , Gene Order , Genes, Mitochondrial , Animals , Base Composition , Evolution, Molecular , Genome Size , Sequence Analysis, DNA
2.
Article in English | MEDLINE | ID: mdl-24845437

ABSTRACT

The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.


Subject(s)
Astacoidea/genetics , DNA, Mitochondrial/genetics , Genome, Mitochondrial , Animals , Australia , Base Composition , Base Sequence , Gene Order , Phylogeny , Sequence Analysis, DNA/veterinary
3.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3329-30, 2016 09.
Article in English | MEDLINE | ID: mdl-25738217

ABSTRACT

The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.


Subject(s)
Astacoidea/classification , Astacoidea/genetics , Genome, Mitochondrial , Animals , Base Composition , Codon , Computational Biology/methods , Gene Order , Genes, Mitochondrial , Genome Size , Open Reading Frames , Sequence Analysis, DNA , Whole Genome Sequencing
4.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(6): 4099-4100, 2016 11.
Article in English | MEDLINE | ID: mdl-25629489

ABSTRACT

The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.


Subject(s)
Anomura/genetics , Crustacea/genetics , Decapoda/genetics , Gene Order/genetics , Genome, Mitochondrial/genetics , Animals , Base Composition/genetics , RNA, Transfer/genetics
5.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(6): 4176-4177, 2016 11.
Article in English | MEDLINE | ID: mdl-25630729

ABSTRACT

Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.


Subject(s)
Decapoda/genetics , High-Throughput Nucleotide Sequencing/methods , Mitochondria/genetics , Sequence Analysis, DNA/methods , Animals , Base Composition , Endangered Species , Gene Order , Genome Size , Genome, Mitochondrial , Open Reading Frames , RNA, Ribosomal/genetics , RNA, Transfer/genetics
6.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3181-3, 2016 09.
Article in English | MEDLINE | ID: mdl-25648916

ABSTRACT

The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.


Subject(s)
Decapoda/genetics , Genome, Mitochondrial , AT Rich Sequence , Animals , Base Composition , Introduced Species , Open Reading Frames , RNA, Ribosomal/genetics , RNA, Transfer/genetics
7.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3179-80, 2016 09.
Article in English | MEDLINE | ID: mdl-25648918

ABSTRACT

The clawed lobster Nephrops norvegicus is an important commercial species in European waters. We have sequenced the complete mitochondrial genome of the species from a partial genome scan using Next-Gen sequencing. The N. norvegicus has a mitogenome of 16,132 base pairs (71.22% A+ T content) comprising 13 protein-coding genes, 2 ribosomal subunit genes, 21 transfer RNAs, and a putative 1259 bp non-coding AT-rich region. This mitogenome is the second fully characterized for the family Nephropidae and the first for the genus Nephrops. The mitogenome gene order is identical to the Maine lobster, Homarus americanus with the exception of the possible loss of the trnI gene.


Subject(s)
Genome, Mitochondrial , Nephropidae/genetics , AT Rich Sequence , Animals , Base Composition , Open Reading Frames , RNA, Ribosomal/genetics , RNA, Transfer/genetics
8.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3220-1, 2016 09.
Article in English | MEDLINE | ID: mdl-25648928

ABSTRACT

The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.


Subject(s)
Bivalvia/classification , Bivalvia/genetics , Genome, Mitochondrial , Animals , Base Composition , Codon , Computational Biology/methods , Genes, Mitochondrial , Genome Size , Open Reading Frames , Regulatory Sequences, Nucleic Acid , Sequence Analysis, DNA , Whole Genome Sequencing
9.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3205-7, 2016 09.
Article in English | MEDLINE | ID: mdl-25693694

ABSTRACT

The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.


Subject(s)
Fishes/genetics , Genome, Mitochondrial , AT Rich Sequence , Animals , Base Composition , Fish Proteins/genetics , RNA, Ribosomal/genetics , RNA, Transfer/genetics
10.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3157-8, 2016 09.
Article in English | MEDLINE | ID: mdl-25693707

ABSTRACT

The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.


Subject(s)
Decapoda/genetics , Genome, Mitochondrial , AT Rich Sequence , Animals , Base Composition , Open Reading Frames , RNA, Ribosomal/genetics , RNA, Transfer/genetics
11.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3155-6, 2016 09.
Article in English | MEDLINE | ID: mdl-25693708

ABSTRACT

The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.


Subject(s)
Genome, Mitochondrial , Palaemonidae/genetics , AT Rich Sequence , Animals , Base Composition , Gene Order , Open Reading Frames , RNA, Ribosomal/genetics , RNA, Transfer/genetics
12.
Genome Announc ; 3(3)2015 May 14.
Article in English | MEDLINE | ID: mdl-25977435

ABSTRACT

Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344 (previously known as P. fluorescens 1855-344). The genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. A biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antiSMASH server.

13.
Genome Announc ; 3(2)2015 Apr 16.
Article in English | MEDLINE | ID: mdl-25883290

ABSTRACT

Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370.

14.
Genome Announc ; 3(2)2015 Mar 26.
Article in English | MEDLINE | ID: mdl-25814609

ABSTRACT

Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The genome of this strain comprises 5,652,224 bp with 5,014 open reading frames, 9 rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and bacteriocin were also identified.

15.
Genome Announc ; 2(6)2014 Nov 06.
Article in English | MEDLINE | ID: mdl-25377711

ABSTRACT

Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (luxI) that is involved in cell-to-cell communication via quorum sensing.

16.
Genome Announc ; 2(5)2014 Oct 09.
Article in English | MEDLINE | ID: mdl-25301654

ABSTRACT

Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine tunicate found in Bidong Island, Terengganu, Malaysia. In this study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain insight into the role of this bacterium and its association with tunicate hosts in a coral reef habitat.

17.
Genome Announc ; 2(3)2014 May 08.
Article in English | MEDLINE | ID: mdl-24812212

ABSTRACT

Shrub willow, Salix spp. and hybrids, is an important bioenergy crop. Here we report the whole-genome sequences and annotation of 13 endophytic bacteria from stem tissues of Salix purpurea grown in nature and from commercial cultivars and Salix viminalis × Salix miyabeana grown in bioenergy fields in Geneva, New York.

18.
Article in English | MEDLINE | ID: mdl-25621282

ABSTRACT

Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.


Subject(s)
Bacterial Proteins/genetics , Evolution, Molecular , Genetic Variation , Genome, Bacterial , Repressor Proteins/genetics , Sphingomonadaceae/genetics , Trans-Activators/genetics , Transcription Factors/genetics , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Gene Expression Regulation, Bacterial , Phylogeny , Quorum Sensing , Repressor Proteins/chemistry , Repressor Proteins/metabolism , Sequence Alignment , Sphingomonadaceae/chemistry , Sphingomonadaceae/classification , Sphingomonadaceae/metabolism , Trans-Activators/chemistry , Trans-Activators/metabolism , Transcription Factors/chemistry , Transcription Factors/metabolism
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