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

Background

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.

Results

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.

Conclusions

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.

Electronic supplementary material

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

Studies on Serum-Fractions

The finding by Hektoen and Welker and by Taylor that the increase of globulin in diphtheric antitoxins was demonstrable by the precipitative reaction was confirmed with the use of antisera prepared by immunizing rabbits with the washed floccules of diphtheric toxoid-antitoxin.

The amount of protein precipitable by diphtheric toxin from antidiphtheric horse-sera in the indicating mixture was found to be roughly proportional to the antitoxic units determined by titration in vitro; but the amount of the component reacting with antiserum prepared against diphtheric antitoxin-globulin does not parallel the antitoxic potency.

Studies on Serum Fractions

Diphtheric antitoxin is precipitable by the precipitating serum prepared with the floccules of diphtheric toxoid-antitoxin (P.V.At.), whereas pneumococcal antibody is precipitated by the precipitating serum prepared with specific precipitates of pneumococcal SSS (P.V.Ab.) in their optimal proportions and also in the range of excessive precipitin. The former precipitating serum absorbs also antipneumococcal antibody from antipneumococcal horse serum, but it is only in the range of the mixtures containing far less antipneumococcal serum than the quantity present in the optimal proportion. The latter precipitating serum absorbs also antitoxin from antidiphtheric horse serum, but this absorption occurs only in the secondary zone and not in the primary or main zone.

Studies on Serum Fractions

In the previous report we have shown that by immunizing rabbits with injections of the washed flocculi of diphtheriatoxoid-antitoxin or the specific precipitate of pneumococcic S.S.S. an antiserum reacting with horse serum can be obtained. Using these antisera, great differences in the antigenic structure were found among antitoxic, antibacterial and normal horse-sera. In this report we have added further results of the test with many samples of different normal as well as immune horse-sera and also with sera taken from horses during the course of immunization.

The designation of “precipitin-versus-antitoxin” (abbreviation: P.V.At.) for the antiserum prepared with flocculi of diphtheriatoxoid-antitoxin and of “precipitin-versus-antibacterial antibody” (abbreviation: P.V.Ab.) for that prepared with a specific precipitate of pneumococcic S.S.S. was used throughout the text and in the tables. For convenience and also for some other reasons, we designated the fraction giving rise to the precipitation against “precipitin-versus-antitoxin” as “A-fraction” and that causing the primary zone against “precipitin-versus-antibacterial antibody” as “B-fraction” or “Felton-fraction.”

Alum-Precipitation of Diphtheria Toxoid (Improvement of Diphtheria Alum-Toxoid)

Precipitation of diphtheria-toxoid by alum depends on the pH under which the precipitate is formed. Purified toxoid requires much less amounts of alum to be precipitated than the original toxoid. One-eighth by volume of 4 per cent solution of alum seems to be sufficient for toxoid purified with calcium-phosphate to precipitate the greater part of the active principle from it. The superiority of the alum-toxoid as an immunizing agent was shown with toxoids purified with calcium-phosphate.