Towards plant pangenomics

Golicz, Agnieszka A.; Batley, Jacqueline; Edwards, David

doi:10.1111/pbi.12499

Cited by 205 publications

(202 citation statements)

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“…Brassica crops display remarkable morphological diversity, and are grown for their inflorescences, axillary buds, leaves and stems. While two reference genomes of B. oleracea are available12, a reference sequence cannot capture the entire gene content of a species owing to structural variants, namely the presence/absence variants (PAVs) and copy number variants3456. Plant reference genomes have been shown to lack a number of agronomically important genes, restricting the gene space available for analysis, for example, in association studies7.…”

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The pangenome of an agronomically important crop plant Brassica oleracea

et al. 2016

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There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

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The pangenome of an agronomically important crop plant Brassica oleracea

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“…There are several approaches to pangenome assembly including: the representation of the whole pangenome in the k-mer space, full de novo genome assemblies, and iterative read mapping and assembly (Golicz et al, 2015).…”

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Construction and analysis of the Brassica oleracea pangenome

Golicz¹

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This thesis describes the construction and analysis of a first Brassica oleracea pangenome. It also presents a pipeline that was developed and implemented in order to build and analyse the pangenome.B. oleracea is a species of high economic importance encompassing crops like broccoli, Brussels sprout, cabbage, cauliflower, kale and kohlrabi. Additionally, it is of high interest to the scientific community because the crops display remarkable morphological and physiological variation and the genetic underpinning of this variation is not fully understood.Recent years have seen an explosion of genome sequencing projects. It has also become clear that there is a significant amount of presence/absence and copy number variation between individuals of the same species, and a reference sequence from a single individual is unable to capture all of the genomic information necessary to fully characterize a species. The term pangenome was coined to describe all the genomic (genic) sequence information found within species.We have hypothesized that some of the phenotypic variation found in the B. oleracea crops might be due to presence/absence variants and therefore we have set out to construct and analyse the B. oleracea pangenome.The pipeline designed was composed of three main steps 1. Pangenome assembly using an iterative mapping and assembly approach and pangenome annotation. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C.S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., Labadie, K., Alberti, A., Charles, M., Arnaud, D., Guo, H., Daviaud, C., Alamery, S., Jabbari, K., Zhao, M., Edger, P.P., Chelaifa, H., Tack, D., Lassalle, G., Mestiri, I., Schnel, N., Le Paslier, M.-C., Fan, G., Renault, V., Bayer, P.E., Golicz, A.A., Manoli, S., Lee, T.-H., Thi, V.H.D., Chalabi, S., Hu, Q., Fan, C., Tollenaere, R., Lu, Y., Battail, C., Shen, J., Sidebottom, C.H.D., Wang, X., Canaguier, A., Chauveau, A., Bérard, A., Deniot, G., Guan, M., Liu, Z., Sun, F., Lim, Y.P., Lyons, E., Town, C.D., Bancroft, I., Wang, X., Meng, J., Ma, J., Pires, J.C., King, G.J., Brunel, D., Delourme, R., Renard, M.,

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“…This observation has raised concerns that a single reference genome cannot represent the entire sequence diversity present in a population , Golicz et al, 2016a. A considerable number of sequences are affected by copy number variations (CNV) (Żmieńko et al, 2014) which are pervasive in all organisms including human (McCarroll andAltshuler, 2007, Iakoubov et al, 2013), maize (SwansonWagner et al, 2010) and cyanobacteria ).…”

Section: Pangenomic Studiesmentioning

confidence: 99%

“…Several approaches to pangenome assembly and analysis have been developed (Golicz et al, 2015a). The traditional approach, first applied in bacteria involves whole genome assembly of all genotypes, followed by individual annotation and comparison of the gene content (Tettelin et al, 2005, Li et al, 2014d).…”

Section: Introductionmentioning

confidence: 99%

“…The traditional approach, first applied in bacteria involves whole genome assembly of all genotypes, followed by individual annotation and comparison of the gene content (Tettelin et al, 2005, Li et al, 2014d). An alternative is a read mapping and assembly approach, where sequence reads are first mapped to an existing reference, and the unmapped reads are then assembled (Golicz et al, 2015a, Golicz et al, 2016b.…”

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The wheat pangenome: assembly and analysis

Cabrera¹,

Daniel²

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Wheat is one of the most important food crops in the world and its continued breeding is essential to achieve the production goals set by FAO in 2050. Breeding programs benefit from the development of genomic resources that reduce time and costs of selection of suitable varieties. Recent evidence has suggested that an important fraction of crop plant genomes exhibits presence-absence variation and cannot be exploited following the single reference paradigm. Pangenomic studies aim to fill this vacuum by creating a complete catalogue of genes in a species and characterizing them. With the release of the first wheat draft genome for cultivar Chinese Spring, we are able to explore the wheat pangenome. In the first chapter I performed a review of the current status of wheat genomics and pangenomic studies. In the second chapter the public wheat reference is assessed for its suitability as the basis of a pangenomic study. Extensive uncollapsed duplicated sequences and the absence of support for some gene models prompted us to reassemble the genome. Both assemblies were then compared and the new assembly was selected for further study. In the third chapter, eighteen wheat cultivars were used to extend the Chinese Spring reference. A metagenomics assembly approach was employed and 350 Mbp of additional sequence absent from the Chinese Spring reference were assembled. These sequences contained over 20,000 additional genes which were classified into core and variable genes and later characterized. The pangenome size was modelled as a function of the number of genomes and functional enrichment of the variable genes showed that these were enriched with genes involved in response to biotic and abiotic stress. In chapter 4, we use the new pangenome to identify over 34.6 million SNPs and further use these SNPs to characterize core and variable genes, to construct a high density genetic map and to assess the relatedness of the cultivars used in this study. We show that the variable genes have a higher SNP density particularly for non-synonymous SNPs. The results show that the synthetic cultivar W7984 is the most divergent accession alongside Chinese Spring. Finally, in chapter 5, the future of pangenomic studies is evaluated with a critique and suggestions to improve the current wheat pangenome.

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Towards plant pangenomics

Cited by 205 publications

References 73 publications

The pangenome of an agronomically important crop plant Brassica oleracea

The pangenome of an agronomically important crop plant Brassica oleracea

Construction and analysis of the Brassica oleracea pangenome

The wheat pangenome: assembly and analysis

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