Dataset Information

Draft genome of the kiwifruit Actinidia chinensis.

ABSTRACT: The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (?) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.

SUBMITTER: Huang S

PROVIDER: S-EPMC4089393 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Draft genome of the kiwifruit Actinidia chinensis.

Huang Shengxiong S Ding Jian J Deng Dejing D Tang Wei W Sun Honghe H Liu Dongyuan D Zhang Lei L Niu Xiangli X Zhang Xia X Meng Meng M Yu Jinde J Liu Jia J Han Yi Y Shi Wei W Zhang Danfeng D Cao Shuqing S Wei Zhaojun Z Cui Yongliang Y Xia Yanhua Y Zeng Huaping H Bao Kan K Lin Lin L Min Ya Y Zhang Hua H Miao Min M Tang Xiaofeng X Zhu Yunye Y Sui Yuan Y Li Guangwei G Sun Hanju H Yue Junyang J Sun Jiaqi J Liu Fangfang F Zhou Liangqiang L Lei Lin L Zheng Xiaoqin X Liu Ming M Huang Long L Song Jun J Xu Chunhua C Li Jiewei J Ye Kaiyu K Zhong Silin S Lu Bao-Rong BR He Guanghua G Xiao Fangming F Wang Hui-Li HL Zheng Hongkun H Fei Zhangjun Z Liu Yongsheng Y

Nature communications 20130101

The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-g ...[more]

PMID: 24136039

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Project description:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS:A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. CONCLUSIONS:Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Dataset Information

Draft genome of the kiwifruit Actinidia chinensis.

Publications

Draft genome of the kiwifruit Actinidia chinensis.

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