scholarly journals OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

2019 ◽  
Vol 47 (W1) ◽  
pp. W59-W64 ◽  
Author(s):  
Stephan Greiner ◽  
Pascal Lehwark ◽  
Ralph Bock
Keyword(s):  
Mitochondrial Genomes ◽  
Genome Database ◽  
Organellar Genomes ◽  
Sequencing Technologies ◽  
Physical Maps ◽  
Large Sets ◽  
Graphical Visualization ◽  
Standard Tool ◽  
Massive Sequencing ◽  
Ncbi Refseq

Abstract Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

scholarly journals OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

2019 ◽  
Author(s):  
Stephan Greiner ◽  
Pascal Lehwark ◽  
Ralph Bock
Keyword(s):  
Mitochondrial Genomes ◽  
List Type ◽  
Genome Database ◽  
Organellar Genomes ◽  
Sequencing Technologies ◽  
Physical Maps ◽  
Large Sets ◽  
Graphical Visualization ◽  
Standard Tool ◽  
Massive Sequencing

Key pointsOGDRAW has become the standard tool for displaying maps of organellar genomesit converts GenBank entries into graphical mapsa new version with improved functionality has been releasedAbstractOrganellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here were present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW has now access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

scholarly journals SMART: Statistical Mitogenome Assembly with Repeats

2019 ◽  
Author(s):  
Fahad Alqahtani ◽  
Ion I. Măndoiu
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Genome Database ◽  
Sequencing Technologies ◽  
Likelihood Model ◽  
Low Coverage

AbstractBy using next-generation sequencing technologies it is possible to quickly and inexpensively generate large numbers of relatively short reads from both the nuclear and mitochondrial DNA contained in a biological sample. Unfortunately, assembling such whole-genome sequencing (WGS) data with standard de novo assemblers often fails to generate high quality mitochondrial genome sequences due to the large difference in copy number (and hence sequencing depth) between the mitochondrial and nuclear genomes. Assembly of complete mitochondrial genome sequences is further complicated by the fact that many de novo assemblers are not designed for circular genomes, and by the presence of repeats in the mitochondrial genomes of some species.In this paper we describe the Statistical Mitogenome Assembly with Repeats (SMART) pipeline for automated assembly of complete circular mitochondrial genomes from WGS data. SMART uses an efficient coverage-based filter to first select a subset of reads enriched in mtDNA sequences. Contigs produced by an initial assembly step are filtered using BLAST searches against a comprehensive mitochondrial genome database, and used as “baits” for an alignment-based filter that produces the set of reads used in a second de novo assembly and scaffolding step. In the presence of repeats, the possible paths through the assembly graph are evaluated using a maximum-likelihood model. Additionally, the assembly process is repeated a user-specified number of times on re-sampled subsets of reads to select for annotation the reconstructed sequences with highest bootstrap support.Experiments on WGS datasets from a variety of species show that the SMART pipeline produces complete circular mitochondrial genome sequences with a higher success rate than current state-of-the art tools, even from low coverage WGS data. The pipeline is available through an easy-to-use web interface at https://neo.engr.uconn.edu/?tool_id=SMART.

scholarly journals OGDA: a comprehensive organelle genome database for algae

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Tao Liu ◽  
Yutong Cui ◽  
Xuli Jia ◽  
Jing Zhang ◽  
Ruoran Li ◽  
...  
Keyword(s):  
Marine Organism ◽  
Structural Characteristics ◽  
Genome Structure ◽  
Evolutionary Relationship ◽  
Uniparental Inheritance ◽  
Genome Database ◽  
Organelle Genome ◽  
Organellar Genomes ◽  
Genome Data ◽  
Plastid Genomes

Abstract Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.

Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies

2020 ◽  
Vol 15 (1) ◽  
pp. 2-16
Author(s):  
Yuwen Luo ◽  
Xingyu Liao ◽  
Fang-Xiang Wu ◽  
Jianxin Wang
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Critical Role ◽  
High Sensitivity ◽  
Biological Properties ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Massive Sequencing ◽  
Generation Sequencing

Transcriptome assembly plays a critical role in studying biological properties and examining the expression levels of genomes in specific cells. It is also the basis of many downstream analyses. With the increase of speed and the decrease in cost, massive sequencing data continues to accumulate. A large number of assembly strategies based on different computational methods and experiments have been developed. How to efficiently perform transcriptome assembly with high sensitivity and accuracy becomes a key issue. In this work, the issues with transcriptome assembly are explored based on different sequencing technologies. Specifically, transcriptome assemblies with next-generation sequencing reads are divided into reference-based assemblies and de novo assemblies. The examples of different species are used to illustrate that long reads produced by the third-generation sequencing technologies can cover fulllength transcripts without assemblies. In addition, different transcriptome assemblies using the Hybrid-seq methods and other tools are also summarized. Finally, we discuss the future directions of transcriptome assemblies.

scholarly journals DaizuBase, an integrated soybean genome database including BAC-based physical maps

2012 ◽  
Vol 61 (5) ◽  
pp. 661-664 ◽  
Author(s):  
Yuichi Katayose ◽  
Hiroyuki Kanamori ◽  
Michihiko Shimomura ◽  
Hajime Ohyanagi ◽  
Hiroshi Ikawa ◽  
...  
Keyword(s):  
Soybean Genome ◽  
Genome Database ◽  
Physical Maps

scholarly journals Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giulio Formenti ◽  
◽  
Arang Rhie ◽  
Jennifer Balacco ◽  
Bettina Haase ◽  
...  
Keyword(s):  
De Novo ◽  
Tissue Type ◽  
Mitochondrial Genomes ◽  
Gene Duplications ◽  
Library Size ◽  
Sequencing Technologies ◽  
Considerable Impact ◽  
Mitochondrial Genome Evolution ◽  
Complete Mitogenome ◽  
Automated Pipeline

Abstract Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

scholarly journals Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia

2017 ◽  
Vol 13 (11) ◽  
pp. 20170570 ◽  
Author(s):  
Chedly Kastally ◽  
Patrick Mardulyn
Keyword(s):  
Mitochondrial Genome ◽  
Sanger Sequencing ◽  
Leaf Beetle ◽  
Universal Primers ◽  
Mitochondrial Genomes ◽  
Single Individual ◽  
Sequencing Technologies ◽  
Pcr Products ◽  
Nucleotide Divergence ◽  
Genomic Variant

Mitochondrial genome heteroplasmy—the presence of more than one genomic variant in individuals—is considered only occasional in animals, and most often involves molecules differing only by a few recent mutations. Thanks to new sequencing technologies, a large number of DNA fragments from a single individual can now be sequenced and visualized separately, allowing new insights into intra-individual mitochondrial genome variation. Here, we report evidence from both (i) massive parallel sequencing (MPS) of genomic extracts and (ii) Sanger sequencing of PCR products, for the widespread co-occurrence of two distantly related (greater than 1% nucleotide divergence, excluding the control region) mitochondrial genomes in individuals of a natural population of the leaf beetle Gonioctena intermedia . Sanger sequencing of PCR products using universal primers previously failed to identify heteroplasmy in this population. Its occurrence was detected with MPS data and may have important implications for evolutionary studies. It suggests the need to re-evaluate, using MPS techniques, the proportion of animal species displaying heteroplasmy.

scholarly journals Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

2020 ◽  
Author(s):  
Giulio Formenti ◽  
Arang Rhie ◽  
Jennifer Balacco ◽  
Bettina Haase ◽  
Jacquelyn Mountcastle ◽  
...  
Keyword(s):  
De Novo ◽  
Tissue Type ◽  
Mitochondrial Genomes ◽  
Gene Duplications ◽  
Library Size ◽  
Sequencing Technologies ◽  
Considerable Impact ◽  
Mitochondrial Genome Evolution ◽  
Complete Mitogenome ◽  
Automated Pipeline

AbstractModern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. As part of the Vertebrate Genomes Project (VGP) we have developed mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (>10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization.

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