Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Jin, Shangkun; Han, Zegang; Hu, Yan; Si, Zhanfeng; Hé, Lǚ; Cheng, Yi‐Kan; Li, Yiqian; Zhao, Ting; Fang, Lei; Zhang, Tianzhen

doi:10.1016/j.molp.2023.02.004

Cited by 20 publications

(5 citation statements)

References 92 publications

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“…Both these elements play a pivotal role in unveiling biological diversity and evolutionary processes at various levels. As a crucial supplement to SNP-based phylogenetics, we have pioneered the development of a phylogenetic research process centered on SVs [23][24][25][26][27] . This process involves the extraction of the most significant and easily distinguishable insertions and deletions.…”

Section: Program Pipelinementioning

confidence: 99%

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

Wang,

Dong,

Liang

et al. 2024

Preprint

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With the explosive growth of biological data, the dimensions of phylogenetic research have expanded to encompass various aspects, including the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge-a robust tool designed to seamlessly integrate the demands of both micro- and macro-evolution, comprehensively utilizing diverse phylogenomic signals, such as genes, SNPs, structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge's groundbreaking innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customizable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants, and fungi, attests to its broad applicability in the field of phylogenetics. In summary, the developmental background and innovative features of PhyloForge position it with significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life.

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Section: Program Pipelinementioning

confidence: 99%

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

Wang,

Dong,

Liang

et al. 2024

Preprint

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“…Recently, several inversion studies have been conducted on crops and fruit plants, including rice (Qin et al, 2021;Stein et al, 2018;Wang et al, 2018Wang et al, , 2023Zhou et al, 2023), soybean (Liu et al, 2020), barley (Jayakodi et al, 2020;Zhang et al, 2023), wheat (Walkowiak et al, 2020), brassica (Boideau et al, 2022;Cai et al, 2021), cotton (Jin et al, 2023;Ma et al, 2021), tomato (Wang et al, 2020) and cucumber (Li et al, 2022) (Hu et al, 2023).…”

Section: Current Status Of Inversion Studies In Plantsmentioning

confidence: 99%

“…Inversions were first identified in Drosophila species through the comparison of genetic linkage maps (Sturtevant, 1921) and further studied in the human genome using the G‐banded karyotype technique (Yunis and Prakash, 1982). Subsequent studies have shown inversions to be widespread across plants (Jin et al ., 2023; Li et al ., 2022; Wang et al ., 2023), human (Chaisson et al ., 2019; Ebert et al ., 2021) and animals (da Silva et al ., 2019; Li et al ., 2021). Inversions are prevalent in plants, representing a significant yet often enigmatic source of genome evolution.…”

Section: The Importance and Progress Of Studies On Inversionsmentioning

confidence: 99%

“…Recently, several inversion studies have been conducted on crops and fruit plants, including rice (Qin et al ., 2021; Stein et al ., 2018; Wang et al ., 2018, 2023; Zhou et al ., 2023), soybean (Liu et al ., 2020), barley (Jayakodi et al ., 2020; Zhang et al ., 2023), wheat (Walkowiak et al ., 2020), brassica (Boideau et al ., 2022; Cai et al ., 2021), cotton (Jin et al ., 2023; Ma et al ., 2021), tomato (Wang et al ., 2020) and cucumber (Li et al ., 2022) (Table 2). These studies highlighted that inversions have a significant impact on environmental adaptation and domestication in plants, by modifying recombination rate, gene expression and linkage disequilibrium.…”

Section: Current Status Of Inversion Studies In Plantsmentioning

confidence: 99%

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Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding

Hu,

Scheben,

Wang

et al. 2023

Plant Biotechnology Journal

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SummaryInversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.

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“…SVs are prevalent in the complex genomes of major crops including wheat (Walkowiak et al 2020), barley (Jayakodi et al 2020) and oilseed rape (Chawla et al 2021). Structural variants were also reported to be associated with important traits including yield and flowering time in oilseed rape (Song et al 2020), fruit flavour in tomato (Li et al 2023) and quality traits in cotton (Jin et al 2023). SVs can alter gene function through several mechanisms including: changes to protein coding sequence, splicing patterns, gene expression levels, or any combination thereof (Zanini et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

Golicz,

Yildiz,

Weber

et al. 2024

Preprint

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Structural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that are known to be associated with a range of crop traits, from yield to flowering behaviour and stress responses. Recently, pangenome graphs have emerged as a powerful framework for analysing genomic data by encoding population- or species-level diversity in one data structure. Pangenome graphs have the potential to serve as unbiased references for downstream applications, including SV genotyping and pan-transcriptomic analyses.In this work, we hypothesized that extensive variation affects transcript quantification and expression quantitative trait locus (eQTL) analysis when relying on a single reference, and that using pangenome graphs can mitigate reference sequence bias.We combined long and short read whole genome sequencing data with expression profiling ofBrassica napus(oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. We demonstrate that pangenome graphs provides a superior framework for eQTL analysis by eliminating single reference bias in gene expression quantification. Combined with the graph-based genotyping of SVs, we identified 240 eQTL-SVs found in close proximity of target loci. These SVs affect expression of genes related to important traits, are often not in linkage with SNPs and represent diversity unaccounted for in classical SNP-based analyses.This study highlights the multiple advantages of graph-based approaches in population-scale studies and provides novel insight into gene expression regulation in an important crop.

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Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Cited by 20 publications

References 92 publications

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals

Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding

Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus

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