Building pangenome graphs

Garrison, Erik; Heumos, Simon; Villani, Flavia; Bao, Zhigui; Tattini, Lorenzo; Hagmann, Jörg; Vorbrugg, Sebastian; Marco-Sola, Santiago; Kubica, Christian; Ashbrook, David G.; Thorell, Kaisa; Rusholme‐Pilcher, Rachel; Liti, Gianni; Rudbeck, Emilio; Nahnsen, Sven; Yang, Zuyu; Moses, Mwaniki N.; Nóbrega, Franklin L.; Wu, Yi; Chen, Hao; Ligt, Joep de; Sudmant, Peter H.; Soranzo, Nicole; Colonna, Vincenza; Williams, Robert W.; Prins, Pjotr

doi:10.1101/2023.04.05.535718

Cited by 53 publications

(48 citation statements)

References 29 publications

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“…To study SVs near the inversion breakpoints at the sequence level, we used one dimensional pangenome graphs and dot plots from the sequence alignments of all inversion scaffolds and a reference sequence (total of 25 sequences for each inversion). For the pangenome graph approach, we used pggb (v0.3.1) 52 to construct graphs and odgi (v0.7.3) 53 to prune the resulting graphs. To ensure that the alignments were of high-quality, we tested multiple combinations of -s (segment length) and -p (percent identity) parameters in the mapping step of pggb.…”

Section: Methodsmentioning

confidence: 99%

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Jamsandekar,

Ferreira,

Pettersson

et al. 2023

Preprint

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Chromosomal inversions are associated with local adaptation in many species. However, questions regarding how they are formed, maintained and impact various other evolutionary processes remain elusive. Here, using a large genomic dataset of long-read and short-read sequencing, we ask these questions in one of the most abundant vertebrates on Earth, the Atlantic herring. This species has four megabase-sized inversions associated with ecological adaptation that correlate with water temperature. The S and N inversion alleles at these four loci dominate in the southern and northern parts, respectively, of the species distribution in the North Atlantic Ocean. By determining breakpoint coordinates of the four inversions and the structural variations surrounding them, we hypothesize that these inversions are formed by ectopic recombination between duplicated sequences immediately outside of the inversions. We show that these are old inversions (>1 MY), albeit formed after the split between Atlantic herring and its sister species, the Pacific herring. They are yet to reach mutation-flux equilibrium, but the large Ne of herring combined with the common occurrence of opposite homozygotes across the species distribution has allowed effective purifying selection to prevent accumulation of genetic load and repeats within the inversions.

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Section: Methodsmentioning

confidence: 99%

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Jamsandekar,

Ferreira,

Pettersson

et al. 2023

Preprint

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“…We built for each species a nucleotide-level reference-free pangenome using the tools that are part of the PanGenome Graph Builder (PGGB; (46)) pipeline. The pangenome graph for P. minimum consisted of over 4 million nodes, totaling 59.8 Mbp in length (Figure 3A), representing approximately 1.3 times the genome size of the species.…”

Section: Resultsmentioning

confidence: 99%

“…This complexity can confound traditional comparative genomics methods, as relying on a single representative for species characterization may lead to biased conclusions, especially if the chosen isolate lies at an extreme of the virulence spectrum. Recently, reference-free sequence-based pangenomes have emerged to address this challenge (46, 56). By encompassing a collection of isolates across the virulence spectrum, pangenomes offer a more comprehensive view of a species’ genomic and functional characteristics.…”

Section: Discussionmentioning

confidence: 99%

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

Garcia,

Morales-Cruz,

Cochetel

et al. 2023

Preprint

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The permanent organs of grapevines (V. viniferaL.), like other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses onEutypa lata,Neofusicoccum parvum, andPhaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection, and recent gene-family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes ofE. lataandP. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes inE. lataandP. minimumglycosyltransferases inN. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.

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“…While many early plant pangenomes focused on variation in gene content (Montenegro et al, 2017), more recent pangenomes (Bayer et al, 2022a) have been graph-based due to the increasing availability of high-quality genome assemblies (Zanini et al, 2021). Bioinformatics tools for constructing SV graphs, such as Minigraph-Catus (Hickey et al, 2023) and PGGB (Garrison et al, 2023), facilitated the presentation of haplotypes of the inversion allele among 15 individuals at the ch2L:17 144 069 position in the D. melanogaster pangenome. Similarly, through the construction of a pangenome-wide inversion graph, Li et al (2022) provided a strategy for selecting parental lines during the establishment of segregating populations between wild and cultivated cucumbers.…”

Section: Current Status Of Inversion Studies In Plantsmentioning

confidence: 99%

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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Building pangenome graphs

Cited by 53 publications

References 29 publications

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

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

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