scholarly journals Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

2016 ◽  
Vol 67 (2) ◽  
pp. 133-147 ◽  
Author(s):  
Krisztián Frank ◽  
Endre Barta ◽  
Nóra Á. Bana ◽  
János Nagy ◽  
Péter Horn ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput ◽  
Cervus Elaphus ◽  
Red Deer ◽  
High Throughput Sequencing ◽  
Complete Mitochondrial Genome ◽  
Phylogenetic Position ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
The Family

scholarly journals Characterization of the mitochondrial genome ofArge bellaWei & Du sp. nov. (Hymenoptera: Argidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6131 ◽  
Author(s):  
Shiyu Du ◽  
Gengyun Niu ◽  
Tommi Nyman ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput Sequencing ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Sequencing Data ◽  
Protein Coding ◽  
High Throughput Sequencing Data ◽  
Rna Genes ◽  
Ancestral Type

We describeArge bellaWei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome ofA. bellahas a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in theA. bellamitochondrial genome as compared to the ancestral type in insects:trnMandtrnQare shuffled, whiletrnWis translocated from thetrnW-trnC-trnYcluster to a location downstream oftrnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except fortrnS1. H821 ofrrnSand H976 ofrrnLare redundant. A phylogenetic analysis based on mitochondrial genome sequences ofA. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.

The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae

2010 ◽  
Vol 81 (5) ◽  
pp. 551-557 ◽  
Author(s):  
Kenta WADA ◽  
Kazuhiro OKUMURA ◽  
Masahide NISHIBORI ◽  
Yoshiaki KIKKAWA ◽  
Michinari YOKOHAMA
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Cervus Elaphus ◽  
Red Deer ◽  
Complete Mitochondrial Genome ◽  
The Family

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

scholarly journals Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 83-90 ◽  
Author(s):  
Yan Guo ◽  
Yulin Dai ◽  
Hui Yu ◽  
Shilin Zhao ◽  
David C. Samuels ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7853 ◽  
Author(s):  
Yuchen Yan ◽  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Qianying Ren ◽  
Shiyu Du ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Morphological Characters ◽  
Trna Genes ◽  
Sequencing Data ◽  
Link Type

Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.

scholarly journals HTSeq - A Python framework to work with high-throughput sequencing data

2014 ◽  
Author(s):  
Simon Anders ◽  
Paul Theodor Pyl ◽  
Wolfgang Huber
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Standard Work ◽  
Data Formats ◽  
High Throughput Sequencing Data ◽  
Python Package

Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data such as genomic coordinates, sequences, sequencing reads, alignments, gene model information, variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability: HTSeq is released as open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index, https://pypi.python.org/pypi/HTSeq

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