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

Abstract

BackgroundMost 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.ResultsA 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.

Carbon starvation reduces carbohydrate and anthocyanin accumulation in red‐fleshed fruit via trehalose 6‐phosphate and MYB27

“…On average, 90% of the reads (Table S5) aligned to the Red5 A. chinensis var. chinensis genome (Pilkington et al ). RNA‐Seq data were validated by qPCR for a selection of 10 gene models; the two methods had a significant Pearson correlation coefficient ( r ) of 0.89 ( p < .0001; Figure S3).…”

“…Kiwifruit TPS gene models were identified by BLAT search (Kent ) of translated protein sequences from the Red5 A. chinensis var. chinensis genome (Pilkington et al ), using the Arabidopsis TPS genes (Lunn ) as queries. Amino acid sequences for deduced kiwifruit and Arabidopsis TPS proteins and the outgroup Escherichia coli OtsA protein (Lunn ) were aligned by Geneious Alignment (Global alignment with free end gaps) in Geneious (R10.0.9; https://www.geneious.com).…”

Mutagenesis of kiwifruit CENTRORADIALIS‐like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering

“…The type of mutations and position of frame shifts were likely to impact on the phenotypes. Small changes in FT and TFL1/CEN-like sequences can reverse their activating or repressing roles in regulation of flowering (Ahn et al, 2006;Ho and Weigel, 2014) and can interfere with flower-activating capacity of other members of the PEBP family (Blackman et al, 2010;Pin et al, 2010). All compact lines had the AcCEN4 E1-E4 deletion and a large insertion was seen in AcCEN that may have rendered line 14 infertile, although it produced terminal flowers indistinguishable from the fertile terminal flowers developing on other early flowering lines.…”

“…These approaches have often proven to be unreliable (Zhang et al, 2010) or failed to promote flowering in fruit crops, affecting other aspects of development instead (Freiman et al, 2015;Varkonyi-Gasic et al, 2013). In contrast, stable mutations in these genes have underpinned domestication of crops such as legumes, sugar beet, sunflower and strawberry (Blackman et al, 2010;Iwata et al, 2012;Kwak et al, 2012;Liu et al, 2010;Pin et al, 2010), or in case of a natural mutation in the CEN homolog SELF PRUNING (Pnueli et al, 1998), revolutionized production and industrial processing of tomato.…”

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

“…The results of this gene structure re-alignment highlight the limits of automated gene annotation and the importance of ongoing curation of gene structure annotations. An example of the importance of manual curation of gene models has recently been reported in kiwifruit, where more than 90% of the in silico predicted gene models were re-annotated compared to a previous draft version 21 . The annotation of the BartlettDHv2.0 assembly has been loaded into the online resource for community annotation of eukaryotes (ORCAE) 22 to facilitate ongoing manual curation of gene models.…”