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

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

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.