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.

Bacteria, tomatoes, and trypanosomes all contain genes for a large protein with extensive homology to the regulatory subunit, ClpA, of the ATP-dependent protease of Escherichia coil, COp. AU members of the family have between 756 and 926 amino acids and contain two large regions, of 233 and 192 amino acids, each containing consensus sequences for nucleotide binding. Within these regions there is at least 85% similarity between the most distant members of the family. The high degree of similarity among the ClpA-like proteins suggests that Clp-like proteases are likely to be important participants in energy-dependent proteolysis in prokaryotic and eukaryotic cells.Energy-dependent proteolysis plays a key role in prokaryotic and eukaryotic cells by regulating the availability of certain short-lived regulatory proteins, ensuring the proper stoichiometry for multi-protein complexes, and ridding the cell of abnormal proteins (1)(2)(3). A homologous energy-dependent protease shared by evolutionarily diverse organisms has not been previously described. In this paper we provide evidence that the regulatory subunit of the ATP-dependent Clp protease of Escherichia coli has been conserved to an unusual degree in numerous prokaryotes and eukaryotes. The Clp protease of E. coli is a two-component ATP-dependent protease that contributes to the turnover of abnormal proteins (4-7). The large ClpA subunit (81,000 kDa) has intrinsic ATPase activity. The smaller ClpP subunit (21,000 (7,9).Sequencing of the cipA gene, encoding the regulatory subunit of the Cip protease, allowed us to discover that ClpA is a member of a family of well-conserved proteins with no previously described function. Members ofthe family include a second E. coli gene, called clpB, and genes from plants, trypanosomes, and Gram-positive and Gram-negative bacteria. E. coli contains two members of the family (see below)as does tomato (E.P., unpublished data) (Fig. 1). § § T. brucei has one gene with DNA sequence homology to the family (M.C., unpublished data); other organisms listed in Fig. 1 have not been tested for the presence of a second gene. Most of these sequences have not previously been published; the presence in the data banks of a fragment of the C terminus of the clpB gene (previously called ORF-BG) allowed others of us encountering homologous sequences to contact the author of the first publication (11) and subsequently contact each other. In the absence of a concerted effort to detect Clp-like genes in eukaryotic or other prokaryotic organisms, the serendipitous discovery of seven such genes and a fragment of an eighth suggests that the family is extremely widespread. The degree of conservation strongly suggests that the members of this family all represent the regulatory subunit for Clp-like energy-dependent proteases, although the possibility exists that the ClpA protein has evolved other ATPdependent regulatory functions as well.The proteins predicted from the DNA sequences of members of this family have two regions of particularly hig...

Apple is an important crop and a focus of research worldwide. However, some aspects of floral commitment and morphogenesis remain unclear. A detailed characterization of bourse shoot apex development was undertaken to provide a framework for future genetic, molecular and physiological studies. Eight morphologically distinct stages of shoot apex development, prior to winter dormancy, were defined. Based on measurements of meristem diameter, two stages of vegetative development were recognized. Vegetative meristems were flat, and either narrow (stage 0) or broad (stage 1). Pronounced doming of the apex marked stage 2. During stage 3, the domed meristem initiated four to six lateral floral meristems and subtending bracts before converting to a terminal floral meristem (stage 4). The terminal floral meristem proceeded directly with bractlet and sepal initiation, while lateral floral meristems initiated bractlets (stage 5). Sepal initiation began on the basal lateral flower (stage 6) and continued in an acropetal direction until all floral meristems had completed sepal initiation (stage 7). In this study, only stage 0 and stage 7 apices were observed in dormant buds, indicating that stages 1-6 are transient. The results suggest that broadening of the apex (stage 1) is the first morphological sign of commitment to flowering.

Phloem-mobile endogenous RNA is trafficked selectively into the shoot apex. In contrast, most viruses and long-distance post-transcriptional gene silencing (PTGS) signals are excluded from the shoot apex. These observations suggest the operation of an underlying regulatory mechanism. To examine this possibility, a potexvirus movement protein, known to modify cell-to-cell trafficking and PTGS, was expressed ectopically in transgenic plants. These plants were found to be compromised in their capacity to exclude both viral RNA and silencing signals from the shoot apex. The transgenic plants also displayed various degrees of abnormal leaf polarity depending on transgene expression level. Normal patterns of organ development were restored by either virus- or Agrobacterium tumefaciens-mediated induction of PTGS. This revealed the presence of an RNA signal surveillance system that acts to allow the selective entry of RNA into the shoot apex. We propose that this surveillance system regulates signaling and protects the shoot apex, in particular the cells that give rise to reproductive structures, from viral invasion.

Leaf primordia initiate from the shoot apical meristem with inherent polarity; the adaxial side faces the meristem, while the abaxial side faces away from the meristem. Adaxial/abaxial polarity is thought to be necessary for laminar growth of leaves, as mutants lacking either adaxial or abaxial cell types often develop radially symmetric lateral organs. The milkweed pod1 (mwp1) mutant of maize (Zea mays) has adaxialized sectors in the sheath, the proximal part of the leaf. Ectopic leaf flaps develop where adaxial and abaxial cell types juxtapose. Ectopic expression of the HD-ZIPIII gene rolled leaf1 (rld1) correlates with the adaxialized regions. Cloning of mwp1 showed that it encodes a KANADI transcription factor. Double mutants of mwp1-R with a microRNA-resistant allele of rld1, Rld1-N1990, show a synergistic phenotype with polarity defects in sheath and blade and a failure to differentiate vascular and photosynthetic cell types in the adaxialized sectors. The sectored phenotype and timing of the defect suggest that mwp1 is required late in leaf development to maintain abaxial cell fate. The phenotype of mwp1; Rld1 double mutants shows that both genes are also required early in leaf development to delineate leaf margins as well as to initiate vascular and photosynthetic tissues.