GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

Mao, Yafei

doi:10.7717/peerj.6303

Cited by 8 publications

(5 citation statements)

References 31 publications

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“…Ancient WGD is usually inferred using the dS-based method, but artificial signals in dS distributions have been reported in previous studies, because of dS saturation (dS value >1) or using poorly annotated genomes or allelic variations or low retention rates (Rabier et al., 2014, Tiley et al., 2016, Vanneste et al., 2012, Mao, 2019). There is an extra peak in the dS distribution of anchor gene pairs in A .…”

Section: Discussionmentioning

confidence: 99%

“…In the past 10 years, next-generation sequencing has generated a wealth of genomic data at vastly decreased cost and reduced efforts (Goodwin et al., 2016, Hardwick et al., 2017). Three main methods were developed to identify WGD, based on (1) analysis of the rate of synonymous substitutions per synonymous site (dS) of duplicated genes within a genome (dS-based method) (Blanc et al., 2003, Lynch and Conery, 2000, Vanneste et al., 2014, Mao, 2019), (2) phylogenetic analysis of gene families among multiple genomes (phylogenomic analysis) (Blomme et al., 2006, Jiao et al., 2011), and (3) synteny block identification compared with sister lineages without WGD (synteny analysis) (Bowers et al., 2003, Dehal and Boore, 2005, Zhang et al., 2017). The dS-based method and phylogenomic analysis only require gene family information, without genome assembly.…”

Section: Introductionmentioning

confidence: 99%

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A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

Mao

Satoh

2019

iScience

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Summary Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora , a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora , concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora .

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

Mao

Satoh

2019

iScience

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“…From the synteny table, gene pairs between C. neglecta and subgenomes of C. sativa as well as A. thaliana were identified and used to calculate the rates of synonymous substitutions per synonymous site ( K s) using GenoDup pipeline (Mao, 2019 ). This pipeline utilized protein and nucleotide sequences of a gene pair to calculate ( K s).…”

Section: Methodsmentioning

confidence: 99%

Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa

Chaudhary

Koh

Perumal

et al. 2022

Plant Biotechnology Journal

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Summary Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome‐level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long‐read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison with C. neglecta, and the complete lack of fractionation of meiosis‐specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement.

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“…For every collinear gene pair in the genome, we calculated the Ks value for each pair. In addition, the Ks value was calculated using the paralogous gene pair generated by orthologous gene clustering using the GenoDup‐Pipeline with “‐n 5” parameter (Mao, 2019). A plant average Ks /year rate of 6.1 × 10 −9 was used to predict the divergence time of the WGD event in diploid plants (Fawcett et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)

Chung

Kim

Bolser

et al. 2021

Molecular Ecology Resources

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Cymbidium goeringii, commonly known as the spring orchid, has long been favoured for horticultural purposes in Asian countries. It is a popular orchid with much demand for improvement and development for its valuable varieties. Until now, its reference genome has not been published despite its popularity and conservation efforts. Here, we report the de novo assembly of the C. goeringii genome, which is the largest among the orchids published to date, using a strategy that combines short‐ and long‐read sequencing and chromosome conformation capture (Hi‐C) information. The total length of all scaffolds is 3.99 Gb, with an N50 scaffold size of 178.2 Mb. A total of 29,556 protein‐coding genes were annotated and 3.55 Gb (88.87% of genome) repetitive sequences were identified. We constructed pseudomolecular chromosomes using Hi‐C, incorporating 89.4% of the scaffolds in 20 chromosomes. We identified 220 expanded and 106 contracted genes families in C. goeringii after divergence from its close relative. We also identified new gene families, resistance gene analogues and changes within the MADS‐box genes, which control a diverse set of developmental processes during orchid evolution. Our high quality chromosomal‐level assembly of C. goeringii can provide a platform for elucidating the genomic evolution of orchids, mining functional genes for agronomic traits and for developing molecular markers for accelerated breeding as well as accelerating conservation efforts.

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GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

Cited by 8 publications

References 31 publications

A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa

A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)

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