ArticleBMC bioinformatics2019
WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.Cell genomics · 2024Article
- Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.BMC genomic data · 2024Article
- PacBio Full-Length Transcriptome of a TetraploidAnimals : an open access journal from MDPI · 2023Article
- Systematic dissection of genomic features determining the vast diversity of conotoxins.BMC genomics · 2023Article
- The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes.Scientific reports · 2023Article
- Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (International journal of molecular sciences · 2023Article
- High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement.Plant communications · 2022Article
- Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications ofFrontiers in plant science · 2022Article
- The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity.GigaScience · 2021Article
- Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis.Molecular biology reports · 2019Article
- The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae).Genome biology and evolution · 2019Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundWith the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method. Here, to resolve these problems, we have designed a universal and simple technical tool WGDdetector for detecting WGDs using either genome or transcriptome annotations in different organisms based on the widely used dS based method.
resultsWe have constructed WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.
conclusionWGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system.
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