The Euscaphis japonica genome and the evolution of malvids

Abstract

SUMMARY Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high‐quality chromosome‐level genome assembly for Euscaphis japonica, an early‐diverging species within malvids. Genome‐based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit‐hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

“…Within rosids, the main conflicts with previous phylogenetic analyses related to the position of Myrtales and the phylogenetic relationships within clade II. Our results indicated that Myrtales are sister to other rosids, which is consistent with most analyses [37,[45][46][47][48][49][50][51][52][53]56] but not with an analysis of 1000 transcriptomes that suggests that Myrtales are nested within other malvids [27]. Within rosid clade II, our results support the hypothesis that Fagales are sister to the other species and Cucurbitales are sister to Fabales, whereas previous studies have concluded that Fagales and Fabales cluster together and Cucurbitales and Rosales are sister clades [27,43,50].…”

Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

“…E. konishii fruit maturation and ripening involve pericarp splitting, pericarp overturn, and the accumulation of secondary metabolites ( Yuan et al, 2018b ; Liang et al, 2019 ; Huang et al, 2019 ; Sun et al, 2021 ). Pericarp overturn, the process in which the pericarp morphological changes after pericarp splitting ( Supplementary Figure S2 ), is the main difference between E. konishii fruits and those of grape ( Vitis vinifera ) and tomato ( Yuan et al, 2018b ; Liang et al, 2019 ; Sun et al, 2021 ), which and may contribute to its survival and enable expansion to new environments ( Sun et al, 2021 ). Pericarp overturn may be the result of uneven cell growth between epicarp and endocarp ( Sun et al, 2021 ), which is associated with cell growth or differentiation ( Ding et al, 2011 ).…”

“…Pericarp overturn, the process in which the pericarp morphological changes after pericarp splitting ( Supplementary Figure S2 ), is the main difference between E. konishii fruits and those of grape ( Vitis vinifera ) and tomato ( Yuan et al, 2018b ; Liang et al, 2019 ; Sun et al, 2021 ), which and may contribute to its survival and enable expansion to new environments ( Sun et al, 2021 ). Pericarp overturn may be the result of uneven cell growth between epicarp and endocarp ( Sun et al, 2021 ), which is associated with cell growth or differentiation ( Ding et al, 2011 ). Auxin asymmetric distribution mediated by development and environmental cues results in uneven cell growth, thus regulating plant growth and response to environmental changes ( Ding et al, 2011 ).…”

“…Hidden Markov model (HMM) logos of Aux/IAA (PF02309) and ARF (PF06507) proteins were downloaded from the Pfam database ( Finn et al, 2014 ) and used to scan the E. konishii predicted proteome ( Sun et al, 2021 ) with the HMMER software package ( Finn et al, 2011 ). The resulting Aux/IAA and ARF candidates were further used to generate HMM logos for EkIAAs and EkARFs using hmm-build from the HMMER suite ( Finn et al, 2011 ), before scanning the E. konishii proteome again.…”

Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

“…The monophyly of the superrosids has been recovered repeatedly in previous studies, with both organellar (Li et al, 2019;Moore et al, 2010;Sun et al, 2015) and nuclear genes (One Thousand Plant Transcriptomes Initiative, 2019;Sun et al, 2021;Zhang et al, 2012), as well as combined datasets (Sun et al, 2020;Wang et al, 2009). However, relationships within the superrosids have proven more problematic.…”