ASolanum lycopersicoidesreference genome facilitates biological discovery in tomato

Abstract

SummaryWild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs). Despite the utility of these wild relatives and their associated ILs, limited finished genomes have been produced to aid genetic and genomic studies. We have generated a chromosome-scale genome assembly for Solanum lycopersicoides LA2951 using PacBio sequencing, Illumina, and Hi-C. We identified 37,938 genes based on Illumina and Isoseq and compared gene function to the available cultivated tomato genome resources, in addition to mapping the boundaries of the S. lycopersicoides introgressions in a set of cv. VF36 x LA2951 introgression lines (IL). The genome sequence and IL map will support the development of S. lycopersicoides as a model for studying fruit nutrient/quality, pathogen resistance, and environmental stress tolerance traits that we have identified in the IL population and are known to exist in S. lycopersicoides.

Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species

“…Homozygous Ptr1/Ptr1 plants are referred to as LA4245‐Ro and LA4277‐Ro, and ptr1/ptr1 plants are referred to as LA4245‐S and LA4277‐S (Mazo‐Molina et al ., 2019). The introgression region shared by LA4245‐R and LA4277‐R contains 16 annotated NLR‐encoding genes in the current assembly of the S. lycopersicoides genome sequence (Powell et al ., 2020). An additional approximately 50 NLR genes occur only in LA4277‐R; the latter genes were not considered as candidates for Ptr1 (Figure 1a).…”

“…The top 10 BLASTp hits of the Ptr1, Mr5 and RPS2 NB‐ARC domains were identified in the S. lycopersicoides v.0.6 genome sequence (Powell et al ., 2020), Malus domestica (GDR GDDH13 V1.1; Jung et al ., 2019) and Arabidopsis thaliana (TAIR Araport 11) genome protein databases. The NB‐ARC domain of each protein hit was determined using Interpro scan (https://www.ebi.ac.uk/interpro/), and the amino acid sequences of the NB‐ARC domain for each species were aligned to check for the presence of the NB‐ARC conserved motifs.…”

“…A genome sequence for S. lycopersicoides LA2951 was generated and used to examine the introgression on chromosome 4 in LA4245 and LA4277 that carries the Ptr1 locus (Mazo‐Molina et al ., 2019; Powell et al ., 2020). A total of 16 genes that encode predicted NLR proteins were annotated in the introgression region shared between LA4245 and LA4277, and we hypothesized that one of these genes was Ptr1 (Mazo‐Molina et al ., 2019).…”

A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding

“…High quality reference genomes are available for the cultivated tomato, S. lycopersicum cv. ‘Heinz 1706’ (SL4.0) (Hosmani et al., 2019; Sato et al., 2012), the closely related red‐fruited Solanum pimpinellifolium ‘LA2093’ (Wang et al., 2020b), the more distantly related green‐fruited Solanum pennellii ‘LA0716’ (Bolger et al., 2014) and the purple/black‐fruited Solanum lycopersicoides ‘LA2951’ (Powell et al., 2020). Alongside these reference genomes, more than 1000 tomato varieties and wild tomato species have been sequenced on Illumina platforms (Aflitos et al., 2014; Gao et al., 2019; Lin et al., 2014) and a panel of 100 of these were recently sequenced using ONT long reads to characterize structural variants (Alonge et al., 2020).…”

A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding

“…High quality reference genomes are available for the cultivated tomato, S. lycopersicum cv. 'Heinz 1706' (SL4.0) (Sato et al, 2012;Hosmani et al, 2019), the closely related red-fruited S. pimpinellifolium 'LA2093' (Wang et al, 2020b), the more distantly related green fruited S. pennellii 'LA0716' (Bolger et al, 2014) and the purple/black fruited S. lycopersicoides 'LA2951' (Powell et al, 2020). Alongside these reference genomes, more than 1000 tomato varieties and wild tomato species have been sequenced on Illumina platforms (Aflitos et al, 2014;Lin et al, 2014;Gao et al, 2019) and a panel of 100 of these were recently sequenced using ONT long reads to characterize structural variants (Alonge et al, 2020).…”