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

• DOI: 10.1186/s12864-018-4656-3
• Publication Date: 2018-04-16T08:31:49Z
• Authors: Sarah M. Pilkington; Ross Crowhurst; Elena Hilario; Simona Nardozza; Lena Fraser; Yongyan Peng; Kularajathevan Gu...; 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 Me...; 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-D...; Charlotte Voogd; Davin Leif; Declan Lafferty; Edwige J. F. Soul...; 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-...; 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 Karunai...; Sean Bulley; Shayhan Chunkath; Zac Hanley; Roy Storey; Amali H. Thrimawi...; Susan Thomson; Charles David; Raffaele Testolin; Hongwen Huang; Roger P. Hellens; Robert J. Schaffer
• Keywords: Actinidia chinensis; Synteny; Gene Annotation; Sequence assembly; Indel; Gene prediction

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