Genome sequence ofJaltomataaddresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae

Abstract

Within the economically important plant family Solanaceae, Jaltomata is a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ~80 species. Here we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long-reads (25X) and Illumina short-reads (148X) achieved an assembly of approximately 1.45 Gb, spanning ~96% of the estimated genome. 96% of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (~80%) of the genome, with the most recently active element, Gypsy, expanding across the genome in the last 1-2 million years.Computational gene prediction, in conjunction with a merged transcriptome dataset from 11 tissues, identified 34725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined that Jaltomata is most likely sister to Solanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression between Jaltomata and Capsicum after these species split. We also identified gene family dynamics specific to Jaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility.This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group, and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.

Nanopore-based genome assembly and the evolutionary genomics of basmati rice

“…T 1 and T 2 can be estimated from the allele combinations of the biallelic sites, where et al, 2015). Calculating T 1 and T 2 for the two conflicting topologies, if P3 is the source of introgression to P1 or P2, then T 2 will be lower in the topology consistent with the introgression; while if P1 or P2 is the source of introgression to P3, then both T 1 and T 2 will be lower in the topology consistent with the introgression (Wu et al, 2018).…”

Inferring the genetic basis of sex determination from the genome of a dioecious nightshade

“…Because the evolution of dioecy obviates the possibility of self-fertilization, this transition might be expected to relax selection to maintain functional selfincompatibility genes; similar losses of self-incompatibility proteins has also been observed in other Solanaceae species that have undergone breeding system transitions (e.g. to selfcompatibility (Wu et al 2019)). Nonetheless, among the genetic changes detected, it is striking that all three of our different approaches detected pectin-related genes in association with sexual differentiation in S. appendiculatum, including pectin acetylesterases (PAE), pectin lyase-like proteins (PLL), and pectin methylesterase inhibitors (PMEI).…”

“…We followed our previous workflow (Wu, et al 2019) to assemble and annotate the genome. In brief, we adopted the MaSuRCA v3.2.2 (Zimin, et al 2017) pipeline to generate the genome assembly, in which relatively high-accuracy Illumina paired-end reads from one male plant (121X coverage from 670-1190) and one female plant (116X coverage from 670-34) were used together to trim and correct low base-call-accuracy long-reads generated by PacBio sequencing from the same two plants (19X coverage from the male 670-1190 and 21X coverage from the female 670-1190).…”

A simple genetic architecture and low constraint allow rapid floral evolution in a diverse and recently radiating plant genus

“…Jaltomata (Schlechtendal; Solanaceae) is the sister genus to the large and economically important Solanum (Olmstead et al ., ; Sarkinen et al ., ; Wu et al ., ), and includes c . 60–80 species distributed from the southwestern United States to the Andean region of South America, in addition to several species endemic to the Greater Antilles and the Galapagos Islands (Miller et al ., ; Mione et al ., ).…”