Actinidia chinensis Assembly and Gene Annotation

About Actinidia chinensis

Actinidia chinensis var. chinensis (2n = 2x = 58) is a fruit tree in the same genus of kiwifruit. It is native to China. This genome corresponds to individual Red5, a diploid F3 sibcross with a predicted inbreeding coefficient of 37.5%, submitted by the New Zealand Institute for Plant and Food Research Ltd.

Assembly

The genome of A. chinensis genotype Red5 was fully sequenced, obtaining a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. The assembly comprises 12,139 contigs anchored in 1,234 scaffolds. Scaffold N50 is 18,944,233 b.

Annotation

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 variety 'Hongyang' in the Kiwifruit Information Resource (KIR v2). 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. Overall, 90.9% had a match with 90% identity or better.

Repeated sequences were called with the Repeat Detector, which is part of the Ensembl Genomes repeat feature pipelines. Repeats length: 204260489 - Repeats content: 36.8%

References

1. A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.
   Pilkington SM, Crowhurst R, Hilario E et al. 2018 . BMC Genomics. 19(1):257.

Picture credit: JJ Harrison. Austin's Ferry, Tasmania, Australia. 42° 46′ 54.48″ S, 147° 15′ 43.81″ E

More information

General information about this species can be found in Wikipedia.