Two Likely Auto-Tetraploidization Events Shaped Kiwifruit Genome and Contributed to Establishment of the Actinidiaceae Family

Abstract

SummaryThe genome of kiwifruit (Actinidia chinensis) was sequenced previously, the first in the Actinidiaceae family. It was shown to have been affected by polyploidization events, the nature of which has been elusive. Here, we performed a reanalysis of the genome and found clear evidence of 2 tetraploidization events, with one occurring ∼50–57 million years ago (Mya) and the other ∼18–20 Mya. Two subgenomes produced by each event have been under balanced fractionation. Moreover, genes were revealed to express in a balanced way between duplicated copies of chromosomes. Besides, lowered evolutionary rates of kiwifruit genes were observed. These findings could be explained by the likely auto-tetraploidization nature of the polyploidization events. Besides, we found that polyploidy contributed to the expansion of key functional genes, e.g., vitamin C biosynthesis genes. The present work also provided an important comparative genomics resource in the Actinidiaceae and related families.

The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant

“…After the divergence of eudicots and monocots, a hexaploidization event (γ event) shared by all core eudicots occurred 140 million years ago (Mya) 32 . Because the Vitis vinifera genome had no additional WGD event except the hexaploidization event and preserved the ancestral eudicot chromosome structure, it has been widely used as a reference genome for the study of evolution [33][34][35] . Actinidia chinensis, the closest genus to Camellia in phylogenetic trees, showed two additional tetraploidization events after the hexaploidization event, namely, the Actinidia recent tetraploidization at~18-20 Mya and the Actinidia ancient tetraploidization at~50-57 Mya 35,36 .…”

“…Because the Vitis vinifera genome had no additional WGD event except the hexaploidization event and preserved the ancestral eudicot chromosome structure, it has been widely used as a reference genome for the study of evolution [33][34][35] . Actinidia chinensis, the closest genus to Camellia in phylogenetic trees, showed two additional tetraploidization events after the hexaploidization event, namely, the Actinidia recent tetraploidization at~18-20 Mya and the Actinidia ancient tetraploidization at~50-57 Mya 35,36 . With the completion of the draft genome sequences of C. sinensis, two opinions regarding WGDs in the C. sinensis genome appeared: that two additional rounds of WGD events occurred in C. sinensis after the hexaploidization event 13 and that only one additional WGD event occurred in C. sinensis independent with tetraploidization in A. chinensis 14,36 .…”

Genome-Wide Analysis of the GRAS Gene Family Exhibited Expansion Model and Functional Differentiation in Sea Buckthorn

“…Colinearity analysis is an important method to analyze plant genome duplication. In recent years, this method has been used to analyze the genome duplication of multiple species [27,28]. In this study, colinear analysis was used for the rst time to correlate the GRAS gene family in sea buckthorn with WGD events.…”

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

“…These duplicated genes provide enormous opportunities for biological innovation [37][38][39]. It has been more and more evident that whole-genome duplications have contributed to the origination, fast divergence [40], establishment of major plant taxa [41,42], such as seed and flowering plants [43], and furthermore the subsets of the latter monocots and dicots [44][45][46][47].…”