A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Authors: Pilkington, Sarah M and Crowhurst, Ross and Hilario, Elena and Nardozza, Simona and Fraser, Lena and Peng, Yongyan and Gunaseelan, Kularajathevan and Simpson, Robert and Tahir, Jibran and Deroles, Simon C and Templeton, Kerry and Luo, Zhiwei and Davy, Marcus and Cheng, Canhong and McNeilage, Mark and Scaglione, Davide and Liu, Yifei and Zhang, Qiong and Datson, Paul and De Silva, Nihal and Gardiner, Susan E and Bassett, Heather and Chagné, David and McCallum, John and Dzierzon, Helge and Deng, Cecilia and Wang, Yen-Yi and Barron, Lorna and Manako, Kelvina and Bowen, Judith and Foster, Toshi M and Erridge, Zoe A and Tiffin, Heather and Waite, Chethi N and Davies, Kevin M and Grierson, Ella P and Laing, William A and Kirk, Rebecca and Chen, Xiuyin and Wood, Marion and Montefiori, Mirco and Brummell, David A and Schwinn, Kathy E and Catanach, Andrew and Fullerton, Christina and Li, Dawei and Meiyalaghan, Sathiyamoorthy and Nieuwenhuizen, Niels and Read, Nicola and Prakash, Roneel and Hunter, Don and Zhang, Huaibi and McKenzie, Marian and Knäbel, Mareike and Harris, Alastair and Allan, Andrew C and Gleave, Andrew and Chen, Angela and Janssen, Bart J and Plunkett, Blue and Ampomah-Dwamena, Charles and Voogd, Charlotte and Leif, Davin and Lafferty, Declan and Souleyre, Edwige J F and Varkonyi-Gasic, Erika and Gambi, Francesco and Hanley, Jenny and Yao, Jia-Long and Cheung, Joey and David, Karine M and Warren, Ben and Marsh, Ken and Snowden, Kimberley C and Lin-Wang, Kui and Brian, Lara and Martinez-Sanchez, Marcela and Wang, Mindy and Ileperuma, Nadeesha and Macnee, Nikolai and Campin, Robert and McAtee, Peter and Drummond, Revel S M and Espley, Richard V and Ireland, Hilary S and Wu, Rongmei and Atkinson, Ross G and Karunairetnam, Sakuntala and Bulley, Sean and Chunkath, Shayhan and Hanley, Zac and Storey, Roy and Thrimawithana, Amali H and Thomson, Susan and David, Charles and Testolin, Raffaele and Huang, Hongwen and Hellens, Roger P and Schaffer, Robert J

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.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.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.

Journal: BMC genomics
DOI: 10.1186/s12864-018-4656-3
Year: 2018

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