scholarly journals TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

2019 ◽  
Author(s):  
Cécile Monat ◽  
Sudharsan Padmarasu ◽  
Thomas Lux ◽  
Thomas Wicker ◽  
Heidrun Gundlach ◽  
...  
Keyword(s):  
Open Source ◽  
Genome Sequence ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Sequencing Data ◽  
Chromosome Conformation ◽  
Assembly Algorithm ◽  
Genome Sequence Assembly ◽  
Mate Pair ◽  
Genomic Studies

AbstractChromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We have developed TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluated the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and constructed an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

scholarly journals TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Cécile Monat ◽  
Sudharsan Padmarasu ◽  
Thomas Lux ◽  
Thomas Wicker ◽  
Heidrun Gundlach ◽  
...  
Keyword(s):  
Open Source ◽  
Genome Sequence ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Sequencing Data ◽  
Chromosome Conformation ◽  
Assembly Algorithm ◽  
Genome Sequence Assembly ◽  
Mate Pair ◽  
Genomic Studies

AbstractChromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

scholarly journals RNA Sequencing Data Sets and Their Whole-Genome Sequence Assembly of Dengue Virus from Three Serial Passages in Vero Cells

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Thidathip Wongsurawat ◽  
Nuntaya Punyadee ◽  
Piroon Jenjaroenpun ◽  
Dumrong Mairiang ◽  
Nattaya Tangthawornchaikul ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Rna Sequencing ◽  
Genome Sequence ◽  
Vero Cells ◽  
Sequence Assembly ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Sequence Assembly

ABSTRACT We present RNA sequencing data sets and their genome sequence assembly for dengue virus that was isolated from a patient with dengue hemorrhagic fever and serially propagated in Vero cells. RNA sequencing data obtained from the first, third, and fifth passages and their corresponding whole-genome sequences are provided in this work.

scholarly journals De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

2009 ◽  
Vol 10 (9) ◽  
pp. R94 ◽  
Author(s):  
Scott DiGuistini ◽  
Nancy Y Liao ◽  
Darren Platt ◽  
Gordon Robertson ◽  
Michael Seidel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Filamentous Fungus ◽  
De Novo ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Illumina Sequence

scholarly journals Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 518
Author(s):  
Zequn Chen ◽  
Xiwu Qi ◽  
Xu Yu ◽  
Ying Zheng ◽  
Zhiqi Liu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Essential Oils ◽  
Gene Family ◽  
Genome Sequence ◽  
Sequence Assembly ◽  
Terpene Synthase ◽  
Genome Sequence Assembly ◽  
Mentha Longifolia ◽  
Specific Expansion ◽  
Species Specific

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

scholarly journals MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5895 ◽  
Author(s):  
Thomas Andreas Kohl ◽  
Christian Utpatel ◽  
Viola Schleusener ◽  
Maria Rosaria De Filippo ◽  
Patrick Beckert ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Sequencing Data ◽  
Desktop Computer

Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.

scholarly journals Limitations of next-generation genome sequence assembly

2010 ◽  
Vol 8 (1) ◽  
pp. 61-65 ◽  
Author(s):  
Can Alkan ◽  
Saba Sajjadian ◽  
Evan E Eichler
Keyword(s):  
Genome Sequence ◽  
Sequence Assembly ◽  
Next Generation ◽  
Genome Sequence Assembly

scholarly journals Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Gereon Schares ◽  
Pratap Venepally ◽  
Hernán A. Lorenzi
Keyword(s):  
Genome Sequence ◽  
Causative Agent ◽  
Definitive Host ◽  
Draft Genome ◽  
Sequence Assembly ◽  
Apicomplexan Parasite ◽  
Draft Genome Sequence ◽  
Besnoitia Besnoiti ◽  
Genome Sequence Assembly ◽  
Bovine Besnoitiosis

ABSTRACT The apicomplexan parasite Besnoitia besnoiti is the causative agent of bovine besnoitiosis that affects livestock, particularly cattle. The definitive host of B. besnoiti is unknown and its transmission only partially understood. Here, we report the first draft genome sequence, assembly, and annotation of this parasite.

Genome sequence assembly: algorithms and issues

Computer ◽  
2002 ◽  
Vol 35 (7) ◽  
pp. 47-54 ◽  
Author(s):  
M. Pop ◽  
S.L. Salzberg ◽  
M. Shumway
Keyword(s):  
Genome Sequence ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Assembly Algorithms
Sign in / Sign up

Export Citation Format

Share Document