The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

Abstract

Background The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. Findings We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. Conclusions This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

“…According to comparative genomics analysis, after the split with A. coerulea , the last common ancestor of core eudicots underwent the γ whole-genome triplication (WGT) event at around 117 million years ago (MYA) [ 39 ]. Furthermore, Brassicaceae species, represented by Arabidopsis, experienced two more WGDs named At-β (60–65 MYA) and At-α (~35 MYA) [ 30 , 40 ], where the At-β WGD was shown to be shared by caperbush, C. violacea , acaya, and spider flower [ 17 , 21 , 22 , 23 ]. In the Capparaceae lineage, caperbush further experienced one independent WGD known as Cs-α at 18.6 MYA [ 21 ].…”

“…Furthermore, Brassicaceae species, represented by Arabidopsis, experienced two more WGDs named At-β (60–65 MYA) and At-α (~35 MYA) [ 30 , 40 ], where the At-β WGD was shown to be shared by caperbush, C. violacea , acaya, and spider flower [ 17 , 21 , 22 , 23 ]. In the Capparaceae lineage, caperbush further experienced one independent WGD known as Cs-α at 18.6 MYA [ 21 ]. In the Cleomaceae lineage, after the split with C. violacea , the last common ancestor of acaya and spider flower first experienced one independent WGD known as Gg-α (~22 MYA), which was followed by an addition of a third genome (Th-α, ~18.4 MYA) to spider flower but not acaya [ 41 ].…”

“…Although it was established that Clade T is absent from papaya ( Carica papaya , Caricaceae) and spider flower ( Tarenaya hassleriana , Cleomaceae) [ 8 ], whether it is present or has been lost in other families within Brassicales is yet to be addressed. Recently available or updated genome assemblies for species in five Brassicales families beyond Brassicaceae, i.e., papaya [ 18 ], horseradish ( Moringa oleifera , Moringaceae) [ 19 ], Bretschneidera sinensis (Akaniaceae) [ 20 ], caperbush ( Capparis spinosa , Capparaceae) [ 21 ], Cleome violacea (Cleomaceae), acaya ( Gynandropsis gynandra , Cleomaceae) [ 22 ], and spider flower [ 23 ], provide a good chance to uncover lineage-specific evolution of the oleosin gene family in this important plant order.…”