Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

Abstract

Potato (Solanum tuberosum L.) is one of the most important crops with a world-wide production of 370 million metric tons. The objectives of this study were (i) to create a high quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (ii) to evaluate the new assembly’s usefulness for various genomic methods and (iii) to assess the performance of phasing in diploid and tetraploid clones, using linked read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity-ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

Genome sequencing of adapted diploid potato clones

“…Reduction of tetraploid breeding clones to diploids is a strategy to generate diploid germplasm, however, genome reduction reveals genetic load that is masked by heterozygosity in tetraploids ( Manrique-Carpintero et al, 2018 ). Genome sequencing of tetraploids show higher levels of deleterious alleles compared to diploids and increased missing genes in each haplotype of a tetraploid compared to the whole genome ( Freire et al, 2021 ; Hoopes et al, 2022 ; Sun et al, 2022 ). The current study describes whole genome sequencing of nine legacy diploid potato clones that were selected from a breeding program for maturity under long-day conditions, pigmentation, disease resistance, tuber appearance and quality among other traits ( De Jong et al, 2003 ; Jung et al, 2005 , 2009 ; Li et al, 2005 ; De Koeyer et al, 2009 ; Tai et al, 2018 ).…”

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes

“…The recently published gene annotation of the diploid clone dAg derived from the elite variety Agria does not contain information about isoforms and partial gene models. Hence, we first improved the existing gene annotation of dAg using the PASA pipeline ( Haas et al, 2003 ) by utilizing the available Iso-Seq data of Agria (tAg; Freire et al, 2021 ) and obtained 44,464 gene models with 58,734 isoforms. We then filtered out partial gene models using AGAT tools ( Dainat et al, 2022 ) and obtained 39,088 full-length gene models with 53,352 isoforms (referred as full-length set in Table 1A ).…”

“…The cultivated potato Solanum tuberosum ssp. tuberosum L. is represented in our study by a diploid clone (hereafter referred to as dAg) which was derived from the tetraploid elite potato cultivar Agria (tAg; Freire et al, 2021 ). The non-cultivated potato clones include Solanum tuberosum L. DM1-3516 R44 (hereafter referred to as DM), which is a doubled monoploid clone derived from the group Phureja ( Pham et al, 2020 ) and Solanum tuberosum L. RH89-039-16 (hereafter referred to as RH) which is a diploid clone derived from a cross between a dihaploid and a diploid potato ( Zhou et al, 2020 ).…”

“…The wild clone in our study is Solanum chacoense M6 (hereafter referred to as M6; Leisner et al, 2018 ). Both the sequence (genome and gene) and annotation files for DM (version 6.1), RH, and M6 were downloaded from http://potato.plantbiology.msu.edu and for dAg was obtained from Freire et al (2021) . In addition, we obtained transposable elements (TEs) annotation for dAg and DM from the above-mentioned sources.…”

“…In this study, we improved the existing gene annotation for dAg using the PASA pipeline v2.5.0 ( Haas et al, 2003 ) followed by classifying the resulting annotation into full-length and partial gene models using AGAT v0.8.0 ( Dainat et al, 2022 ). In that procedure, we used transcriptome datasets generated as part of dAg genome sequencing ( Freire et al, 2021 ) to improve the existing gene annotations.…”