Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits.

Autor:	Lu XM; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Yu XF; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Li GQ; Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China., Qu MH; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Wang H; Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China., Liu C; Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China., Man YP; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Jiang XH; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Li MZ; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Wang J; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Chen QQ; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Lei R; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Zhao CC; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Zhou YQ; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China., Jiang ZW; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Li ZZ; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Zheng S; Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China., Dong C; College of Agricultural Sciences, Xichang University, Xichang, Sichuan, China., Wang BL; Department of Horticulture, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China., Sun YX; College of Life Sciences, Langfang Normal University, Langfang, Hebei, China., Zhang HQ; Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China., Li JW; Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China., Mo QH; Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China., Zhang Y; Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi'an, Shaanxi, China., Lou X; Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China., Peng HX; Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China., Yi YT; Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China., Wang HX; Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China., Zhang XJ; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Wang YB; Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China., Wang D; College of Agriculture, Eastern Liaoning University, Dandong, Liaoning, China., Li L; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Zhang Q; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China., Wang WX; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China., Liu Y; State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China. Electronic address: liuyb@craes.org.cn., Gao L; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China. Electronic address: leigao@wbgcas.cn., Wu JH; The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand. Electronic address: wujinhu8@outlook.com., Wang YC; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China. Electronic address: kiwifruit@wbgcas.cn.
Jazyk:	angličtina
Zdroj:	Plant communications [Plant Commun] 2024 Jun 10; Vol. 5 (6), pp. 100856. Date of Electronic Publication: 2024 Mar 02.
DOI:	10.1016/j.xplc.2024.100856
Abstrakt:	Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta. (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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