Wolfberry genomes and the evolution of Lycium (Solanaceae)

Abstract

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

“…Ancient polyploidy events (also known as WGDs) and additional recent lineage-specific WGDs have presumably caused varying numbers of R2R3-MYB genes within land plants [46]. A recent study sequenced and released the genome of the wolfberry (Lycium bararum L.), an economically important genus of the Solanaceae family [39]. However, this study identifies the first R2R3-MYB gene family from the wolfberry genome and reports a comparative analysis of the R2R3-MYB gene family in five Solanaceae species.…”

“…To date, genome sequences of five Solanaceae species have been sequenced and released, including wolfberry (L. barbarum), tomato (S. lycopersicum), pepper (C. annuum), potato (S. tuberosum), and eggplant (S. melongena) [39][40][41][42][43]. These genomic resources are informative for comparative analyses of the R2R3-MYB gene family among the Solanaceae species.…”

Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review

“…According to Zhao et al (2019) and Rehman et al (2020), the number of genotypes (aa × bb) in the parent (L. barbarum × L. chinense) is 17,513 (17.02%) and 24,329 (59.9%), respectively, indicating that the F 2 and BC1 populations can be used to generate genetic maps and map QTLs in Lycium species. Furthermore, using the newly published (Cao et al, 2021) L. barbarum genome by Cao et al (2021) as a reference genome, we can map QTLs using a more cost-effective method, such as BSA.…”

“…The detected QTLs could be developed as markers for determinate terminal trait selection in Lycium species, which will accelerate the selection of flower terminal cultivars. Moreover, the publication of the genome of L. barbarum (Cao et al, 2021) enables the mining of candidate genes for further study, such as candidate gene validation, rapid breeding of cultivars with determinate flower terminal using transgenic technology, and studies on the mechanism of terminals flower development.…”

Chromosome‐level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae

“…The pepino belongs to the Solanaceae family, which contains approximately 95 genera and 2300 species (Cao et al., 2021). The genomes of several species in this family have been reported, including tomato ( Solanum pennellii , Solanum lycopersicum , and Solanum pimpinellifolium ) (Bolger et al., 2014; International Tomato Genome Sequencing Consortium, 2012; Schmidt et al., 2017; Takei et al., 2021; Wang et al., 2020), potato ( Solanum tuberosum , Solanum phureja ) (Pham et al., 2020; Xu et al., 2011; Zhou et al., 2020), pepper ( Capsicum baccatum , Capsicum chinense , and Capsicum annuum ) (Kim et al., 2014; Kim, Park, et al., 2017; Qin et al., 2014), eggplant ( Solanum melongena ) (Barchi et al., 2019, 2021; Hirakawa et al., 2014; Wei et al., 2020), tobacco ( Nicotiana tabacum , Nicotiana attenuate , Nicotiana sylvestris , Nicotiana tomentosiformis ) (Sierro et al., 2013; Sierro et al., 2014; Xu et al., 2017), wolfberry ( Lycium barbarum , Lycium ruthenicum ) (Cao et al., 2021), and Petunia species ( Petunia axillaris , Petunia inflata ) (Bombarely et al., 2016). However, the pepino genome has not been analyzed until now.…”