Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits
Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved..
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.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2024 |
|---|---|
| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2024 |
|---|---|
| Enthalten in: |
Plant communications - (2024) vom: 02. März, Seite 100856 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Lu, Xue-Mei [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Adaptive evolution |
|---|
| Anmerkungen: |
Date Revised 04.04.2024 published: Print-Electronic Citation Status Publisher |
|---|
| doi: |
10.1016/j.xplc.2024.100856 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM369216512 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM369216512 | ||
| 003 | DE-627 | ||
| 005 | 20240405233716.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 240304s2024 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.xplc.2024.100856 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1366.xml |
| 035 | |a (DE-627)NLM369216512 | ||
| 035 | |a (NLM)38431772 | ||
| 035 | |a (PII)S2590-3462(24)00085-3 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Lu, Xue-Mei |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits |
| 264 | 1 | |c 2024 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Revised 04.04.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status Publisher | ||
| 520 | |a Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a GEA | |
| 650 | 4 | |a adaptive evolution | |
| 650 | 4 | |a dioecism | |
| 650 | 4 | |a kiwiberry | |
| 650 | 4 | |a paleoclimate | |
| 650 | 4 | |a rapid softening | |
| 700 | 1 | |a Yu, Xiao-Fen |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Guo-Qiang |e verfasserin |4 aut | |
| 700 | 1 | |a Qu, Ming-Hao |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Huan |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Chuang |e verfasserin |4 aut | |
| 700 | 1 | |a Man, Yu-Ping |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Xiao-Han |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Mu-Zi |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Jian |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Qi-Qi |e verfasserin |4 aut | |
| 700 | 1 | |a Lei, Rui |e verfasserin |4 aut | |
| 700 | 1 | |a Zhao, Cheng-Cheng |e verfasserin |4 aut | |
| 700 | 1 | |a Zhou, Yun-Qiu |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Zheng-Wang |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Zuo-Zhou |e verfasserin |4 aut | |
| 700 | 1 | |a Zheng, Shang |e verfasserin |4 aut | |
| 700 | 1 | |a Dong, Chang |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Bai-Lin |e verfasserin |4 aut | |
| 700 | 1 | |a Sun, Yan-Xiang |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Hui-Qin |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Jie-Wei |e verfasserin |4 aut | |
| 700 | 1 | |a Mo, Quan-Hui |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Ying |e verfasserin |4 aut | |
| 700 | 1 | |a Lou, Xin |e verfasserin |4 aut | |
| 700 | 1 | |a Peng, Hai-Xu |e verfasserin |4 aut | |
| 700 | 1 | |a Yi, Ya-Ting |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, He-Xin |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Xiu-Jun |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Yi-Bo |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Dan |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Qiong |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Wen-Xia |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Yongbo |e verfasserin |4 aut | |
| 700 | 1 | |a Gao, Lei |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Jin-Hu |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Yan-Chang |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Plant communications |d 2020 |g (2024) vom: 02. März, Seite 100856 |w (DE-627)NLM312622589 |x 2590-3462 |7 nnns |
| 773 | 1 | 8 | |g year:2024 |g day:02 |g month:03 |g pages:100856 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.xplc.2024.100856 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |j 2024 |b 02 |c 03 |h 100856 | ||