A common whole-genome paleotetraploidization in Cucurbitales

Abstract

Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologues and paralogues and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization (BCT) and the allopolyploid nature of the Cucurbitales common tetraploidization (CCT) and the Cucurbita specific tetraploidization (CST). Moreover, we constructed the ancestral Cucurbitales karyotype (ACK-I) comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype (ACK-II) with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.

Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima

“…The Multiple Collinearity Scan toolkit (MCScanX) program (Wang et al, 2012) and writing script were used to conduct collinearity analysis of chestnut genome to determine the duplication model of CmbHLHs (Yu et al, 2021). MCScanX could identify most duplication types except WGD and segmental duplication, and the reason was that the plant genome undergone a large number of chromosome recombination after WGD, which made them difficult to distinguish (Figure 5) (Wang et al, 2018;Yu et al, 2022a;Wang et al, 2022;Yu et al, 2023). As in our previous study (Yu et al, 2023), by drawing the homologous collinearity dot-plot within chestnut genome labeled with the median Ks of the homologous blocks, combining their length and complementarity, WGD and segmental duplications were finally distinguished (Figure 6).…”

Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant

“…Additionally, the leaves, stems, fruit pulp and root bark are often important components as well ( Yu et al, 2018 ). However, the current phylogenetic studies of Cucurbitaceae primarily rely on chloroplast genes and a limited number of nuclear gene molecular markers ( Kousar & Park, 2023 ; Park et al, 2021 ; Renner, Schaefer & Kocyan, 2007 ; Wang et al, 2022a ). As a result, the relationships between the main branches and genera within the family are not clearly understood.…”