A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives

Abstract

There are over 100 known species of cultivated potatoes and their wild relatives. Many of these species, including cultivated potatoes, share the A genome; these species are mainly distributed in South America and are reproductively isolated from Mexican diploid species. The only diploid A-genome species distributed in Mexico is Solanum verrucosum Schlechtendal, which is also a maternal progenitor of Mexican polyploid species. In this study, we constructed a high-quality de novo assembly of the S. verrucosum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. A monohaploid clone (2n=x=12) of S. verrucosum was used to reduce assembly difficulty due to the heterozygous nature of the species. The final sequence assembly consisted of 780.2 Mb of sequence, 684.0 Mb of which were anchored to the 12 chromosomes, with a scaffold N50 of 55.2 Mb. Putative centromeres were identified using publicly available data obtained via chromatin immunoprecipitation sequencing against a centromere-specific histone 3 protein. Transposable elements accounted for approximately 61.8% (482.1 Mb) of the genome, and 46,904 genes were functionally annotated. High gene synteny and similarity were revealed among the genomes of S. verrucosum, S. commersonii, S. chacoense, S. phureja, S. tuberosum, and S. lycopersicum. The reference-quality S. verrucosum genome will provide new insights into the evolution of Mexican polyploid species and contribute to potato breeding programs.

Diversity of Late Blight Resistance Genes in the VIR Potato Collection

“…Quite apart stands S. verrucosum ; this North American species is combined by taxonomists in one clade with the southern South American Tuberosa [ 48 , 101 , 102 ]. Such treatment is not recognized universally, and Bukasov [ 46 ] even put this species into the separate series Verrucosa .…”

A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes

“…High-molecular-weight DNA was extracted, qualified, and used for HiFi read sequencing using the PacBio Sequel lle system (PacBio) as previously described ( Hosaka et al 2022 ). The bam files were converted to a FASTQ file using BAM2fastx 1.3.1 (PacBio) and used for genome assembly with the Hifiasm 0.16.1-r375 assembler ( Cheng et al 2021 ).…”

“…Heinz 1706 SL5.0; Zhou et al 2022 ), S. etuberosum Lindl. (PG0019 [PI 558302]; Tang et al 2022 ), S. verrucosum (11H23 [PI 666968]; Hosaka et al 2022 ), S. chacoense Bitter (M6 v5; Leisner et al 2018 , http://spuddb.uga.edu/M6_v5_0_download.shtml ), S. multidissectum Hawkes [PG5068, (PI 458379, described as S. candolleanum Berthault in Spooner et al 2014 ); Tang et al 2022 ], and S. phureja (DM v8.1, Yang et al 2023 ). Chromosomal sequences of these seven genomes were used for pairwise alignment by Minimap2 ( Li 2018 ) and outputted as SAM and PAF files by defining “-ax asm5 -eqx” and “-x ams5” options, respectively.…”

“…A naturally chromosome-doubled monohaploid clone of S. bulbocastanum (2 n = 2 x = 24) was used to reduce the complexity caused by the heterozygous nature of the species. This is the Mexican diploid species’ first de novo chromosome-scale assembly except for S. verrucosum , the only diploid A-genome species distributed in Mexico ( Hosaka et al 2022 ). The chromosome-scale assemblies facilitated to reveal structural differences between the S. bulbocastanum genome and the previously reported S. phureja , S. multidissectum , S. verrucosum , S. chacoense , S. etuberosum , and S. lycopersicum genomes ( Leisner et al 2018 ; Hosaka et al 2022 ; Tang et al 2022 ; Zhou et al 2022 ; Yang et al 2023 ) in the Potato, Etuberosum, and Tomato clades.…”

“…Molecular analyses revealed clear genome differentiation of Mexican diploid species from the A-genome species ( Hosaka et al 1984 ; Spooner et al 1991 , 2008 ; Pendinen et al 2008 ; Rodríguez and Spooner 2009 ). Recent advancement in nucleotide sequencing technologies allows comparing whole-genome sequences of the tuber-bearing Solanum species ( Aversano et al 2015 ; Leisner et al 2018 ; Zhou et al 2020 ; Tiwari et al 2021 ; Yan et al 2021 ; Hoopes et al 2022 ; Hosaka et al 2022 ; Sun et al 2022 ), which revealed a monophyletic origin of Mexican diploid species sharing the common ancestor with A-genome species ( Li et al 2018 ; Huang et al 2019 ; Gagnon et al 2022 ; Tang et al 2022 ).…”