scholarly journals Complete Mitochondrial and Plastid DNA Sequences of the Freshwater Green Microalga Medakamo hakoo

2021 ◽  
Author(s):  
Mari Takusagawa ◽  
Shoichi Kato ◽  
Sachihiro Matsunaga ◽  
Shinichiro Maruyama ◽  
Yayoi Tsujimoto-Inui ◽  
...  
Keyword(s):  
Green Alga ◽  
Dna Sequences ◽  
Plastid Dna ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
Organellar Genome ◽  
Green Microalga

Here we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Evolution of Pulmonate Gastropod Mitochondrial Genomes: Comparisons of Gene Organizations of Euhadra, Cepaea and Albinaria and Implications of Unusual tRNA Secondary Structures

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 749-758 ◽  
Author(s):  
Nika Yamazaki ◽  
Rei Ueshima ◽  
Jonathan A Terrett ◽  
Shin-ichi Yokobori ◽  
Masayuki Kaifu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Overlapping Genes ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Protein Coding Genes ◽  
Editing Process ◽  
Pulmonate Gastropod

Complete gene organizations of the mitochondrial genomes of three pulmonate gastropods, Euhadra herklotsi, Cepaea nemoralis and Albinaria coerulea, permit comparisons of their gene organizations. Euhadra and Cepaea are classified in the same superfamily, Helicoidea, yet they show several differences in the order of tRNA and protein coding genes. Albinaria is distantly related to the other two genera but shares the same gene order in one part of its mitochondrial genome with Euhadra and in another part with Cepaea. Despite their small size (14.1 – 14.5 kbp), these snail mtDNAs encode 13 protein genes, two rRNA genes and at least 22 tRNA genes. These genomes exhibit several unusual or unique features compared to other published metazoan mitochondrial genomes, including those of other molluscs. Several tRNAs predicted from the DNA sequences possess bizarre structures lacking either the T stem or the D stem, similar to the situation seen in nematode mt-tRNAs. The acceptor stems of many tRNAs show a considerable number of mismatched basepairs, indicating that the RNA editing process recently demonstrated in Euhadra is widespread in the pulmonate gastropods. Strong selection acting on mitochondrial genomes of these animals would have resulted in frequent occurrence of the mismatched basepairs in regions of overlapping genes.

scholarly journals Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Christopher D. Herren ◽  
Alexandra Peister ◽  
Timothy S. Breton ◽  
Maggie S. Hill ◽  
Marcy S. Anderson ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Putative Protein ◽  
Protein Coding Genes

ABSTRACT Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect Mycobacterium smegmatis mc2155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases, cro, immunity repressors, and excise genes involved in the establishment of lysogeny.

scholarly journals Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga Botryococcus braunii Race B (Showa)

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Olga Blifernez-Klassen ◽  
Daniel Wibberg ◽  
Anika Winkler ◽  
Jochen Blom ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Green Alga ◽  
Botryococcus Braunii ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Total Length ◽  
Green Microalga ◽  
Long Chain ◽  
Hydrocarbon Oil

The green alga Botryococcus braunii is capable of the production and excretion of high quantities of long-chain hydrocarbons and exopolysaccharides. In this study, we present the complete plastid and mitochondrial genomes of the hydrocarbon-producing microalga Botryococcus braunii race B (Showa), with a total length of 156,498 and 129,356 bp, respectively.

scholarly journals The Complete Mitochondrial Genome of The American Palm Cixiid, Haplaxius Crudus (Hemiptera: Cixiidae)

2020 ◽  
Author(s):  
Lidia Komondy ◽  
Jose Huguet-Tapia ◽  
Marina S. Ascunce ◽  
Ericka Helmick ◽  
Erica M. Goss ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Internal Control ◽  
Dna Sequences ◽  
Complete Mitochondrial Genome ◽  
Insect Pest ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
American Palm

Abstract Background Haplaxius crudus (the American palm cixiid) is a major insect pest of various economically important palms. H. crudus persists in tropical and subtropical regions where it is known to transmit the lethal yellowing (LY) phytoplasma. It has been implicated as the putative vector of Lethal bronzing (LB), a destructive phytoplasma-induced palm disease affecting over 16 species of ornamental and agricultural palms. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. Analysis of mitochondrial DNA sequences of H. crudus has proven useful for proper species diagnosis and population studies which could benefit management programs aimed at moving infective insects. These analyses describe the first mitochondrial genome from the American palm cixiid, Haplaxius crudus and an insect in the family Cixiidae. Results In this study, the complete mitochondrial genome of H. crudus was assembled and characterized from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator supercomputer. The circular mitogenome of H. crudus is 15,845 bp long and encodes 37 mitochondrial genes (including 13 protein coding genes (PCGs), 22 tRNAs and 2 rRNAs) in addition to a putative non-coding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A and T (44.8 %A, 13.4 %C, 8.5 %G and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is identical to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis indicated that H. crudus is closely related to the planthopper in the family Delphacidae: N. lugens, which is the established sister group to Cixiidae. Conclusions Our studies have elucidated the first reference mitochondrial genome of Haplaxius crudus, providing structural analysis of the circular genome and encoded gene regions. The present results provide future opportunities to assess the diversity and origin of H. crudus. This study demonstrates the significance of understanding the structure and function of the mitochondrial genome to inform effective diagnostic and management strategies for insect pests.

scholarly journals Complete Genome Sequences of 12 B1 Cluster Mycobacteriophages, Gareth, JangoPhett, Kailash, MichaelPhcott, PhenghisKhan, Phleuron, Phergie, PhrankReynolds, PhrodoBaggins, Phunky, Vaticameos, and Virapocalypse

2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Kristofer A. Apellido ◽  
Divya Balchander ◽  
Matthew C. Erlich ◽  
Jakub K. Gocal ◽  
Wiktoria A. Gocal ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Complete Genome ◽  
Soil Samples ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Putative Protein ◽  
Protein Coding Genes

Twelve B1 cluster mycobacteriophages were isolated from soil samples collected in Philadelphia, PA, USA, using Mycobacterium smegmatis mc2 155 as a host, and were sequenced. The genome sequences range in size from 66,887 bp to 68,953 bp in length and have between 99 and 105 putative protein-coding genes.

Accurate annotation of protein-coding genes in mitochondrial genomes

2017 ◽  
Vol 106 ◽  
pp. 209-216 ◽  
Author(s):  
Marwa Al Arab ◽  
Christian Höner zu Siederdissen ◽  
Kifah Tout ◽  
Abdullah H. Sahyoun ◽  
Peter F. Stadler ◽  
...  
Keyword(s):  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Overlapping protein-coding genes in human genome and their coincidental expression in tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao-Hsin Chen ◽  
Chao-Yu Pan ◽  
Wen-chang Lin
Keyword(s):  
Human Genome ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Human Protein ◽  
Clear Understanding ◽  
Overlapping Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Overlapping Gene

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

scholarly journals Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14

2020 ◽  
Vol 10 (7) ◽  
pp. 2131-2140
Author(s):  
Ramisah Mohd Shah ◽  
Angela H. Williams ◽  
James K. Hane ◽  
Julie A. Lawrence ◽  
Lina M. Farfan-Caceres ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Dna Sequences ◽  
Genome Assembly ◽  
Ascochyta Blight ◽  
Ascochyta Rabiei ◽  
Causal Organism ◽  
Protein Coding ◽  
Putative Protein ◽  
Genomic Regions ◽  
Genome Assemblies

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

scholarly journals Mitochondrial Genome Sequences of Diorhabda carinata and Diorhabda carinulata, Two Beetle Species Introduced to North America for Biological Control

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
A. R. Stahlke ◽  
A. Z. Ozsoy ◽  
D. W. Bean ◽  
P. A. Hohenlohe
Keyword(s):  
Biological Control ◽  
North America ◽  
Mitochondrial Genome ◽  
Noncoding Region ◽  
Beetle Species ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Genome Assemblies

We announce the complete circularized mitochondrial genome assemblies of Diorhabda carinata and Diorhabda carinulata, beetle species introduced to North America for the biological control of invasive shrubs of the genus Tamarix L. (Tamaricaceae). The assemblies (16,232 and 16,298 bp, respectively) each comprise 13 protein-coding genes, 22 tRNAs, two rRNAs, and a noncoding region.

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