Secreted peptide ligands are known to play key roles in the regulation of plant growth, development, and environmental responses. However, phenotypes for surprisingly few such genes have been identified via loss-of-function mutant screens. To begin to understand the processes regulated by the CLAVATA3 (CLV3)/ESR (CLE) ligand gene family, we took a systems approach to gene identification and gain-of-function phenotype screens in transgenic plants. We identified four new CLE family members in the Arabidopsis (Arabidopsis thaliana) genome sequence and determined their relative transcript levels in various organs. Overexpression of CLV3 and the 17 CLE genes we tested resulted in premature mortality and/or developmental timing delays in transgenic Arabidopsis plants. Overexpression of 10 CLE genes and the CLV3 positive control resulted in arrest of growth from the shoot apical meristem (SAM). Overexpression of nearly all the CLE genes and CLV3 resulted in either inhibition or stimulation of root growth. CLE4 expression reversed the SAM proliferation phenotype of a clv3 mutant to one of SAM arrest. Dwarf plants resulted from overexpression of five CLE genes. Overexpression of new family members CLE42 and CLE44 resulted in distinctive shrub-like dwarf plants lacking apical dominance. Our results indicate the capacity for functional redundancy of many of the CLE ligands. Additionally, overexpression phenotypes of various CLE family members suggest roles in organ size regulation, apical dominance, and root growth. Similarities among overexpression phenotypes of many CLE genes correlate with similarities in their CLE domain sequences, suggesting that the CLE domain is responsible for interaction with cognate receptors.

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.

Background: Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs).

We have characterized the tomato (Lycopersicon esculentum Mill.) MADS box gene TM29 that shared a high amino acid sequence homology to the Arabidopsis SEP1, 2, and 3 (SEPALLATA1, 2, and 3) genes. TM29 showed similar expression profiles to SEP1, with accumulation of mRNA in the primordia of all four whorls of floral organs. In addition, TM29 mRNA was detected in inflorescence and vegetative meristems. To understand TM29 function, we produced transgenic tomato plants in which TM29 expression was down-regulated by either cosuppression or antisense techniques. These transgenic plants produced aberrant flowers with morphogenetic alterations in the organs of the inner three whorls. Petals and stamens were green rather than yellow, suggesting a partial conversion to a sepalloid identity. Stamens and ovaries were infertile, with the later developing into parthenocarpic fruit. Ectopic shoots with partially developed leaves and secondary flowers emerged from the fruit. These shoots resembled the primary transgenic flowers and continued to produce parthenocarpic fruit and additional ectopic shoots. Based on the temporal and spatial expression pattern and transgenic phenotypes, we propose that TM29 functions in floral organ development, fruit development, and maintenance of floral meristem identity in tomato.Flower development has been the subject of intensive studies over the last decade, particularly in the model plants Arabidopsis and snapdragon (Antirrhinum majus). These studies led to the formulation of the ABC model of floral organ identity, which explained the activities of three classes of genes in specifying the identity of floral organs (Weigel and Meyerowitz, 1994). This model has been supported by genetic and molecular data in a wide range of angiosperm species.According to the ABC model, expression of a class A gene specifies the formation of sepals (the first whorl organ); in combination with the class B genes expression, specifies petal formation. Expression of class B genes and a class C gene specifies stamen identity, whereas expression of C alone determines a carpel identity (Coen and Meyerowitz, 1991;Weigel and Meyerowitz, 1994). Most of the ABC genes belong to the MADS box family (Yanofsky et al., 1990;Jack et al., 1992;Mandel et al., 1992;Goto and Meyerowitz, 1994).Although the ectopic expressions of the ABC genes are sufficient to determine various floral organ identities within the floral meristem, they are insufficient to convert vegetative leaves to floral organs. This suggested that other regulators, in addition to the ABC genes, are required for floral organ specification. Recently, a group of three related MADS box genes SEP 1, 2, and 3 (SEPALLATA 1, 2, and 3) were shown to be necessary for the activity B and C class genes in the control of floral organ formation. First, the SEP1, SEP2, and SEP3 (formerly AGL2, AGL4, and AGL9) redundantly control the activities of the B and C organ identity genes in Arabidopsis because the triple mutant sep1sep2sep3 flower consists entirely of sepals. The sep1/2/...

MYB transcription factors (TFs) regulate diverse plant developmental processes and understanding their roles in controlling pigment accumulation in fruit is important for developing new cultivars. In this study, we characterised kiwifruit TFMYB7, which was found to activate the promoter of the kiwifruit lycopene beta-cyclase (AdLCY-β) gene that plays a key role in the carotenoid biosynthetic pathway. To determine the role of MYB7, we analysed gene expression and metabolite profiles in Actinidia fruit which show different pigment profiles. The impact of MYB7 on metabolic biosynthetic pathways was then evaluated by overexpression in Nicotiana benthamiana followed by metabolite and gene expression analysis of the transformants. MYB7 was expressed in fruit that accumulated carotenoid and Chl pigments with high transcript levels associated with both pigments. Constitutive over-expression of MYB7, through transient or stable transformation of N. benthamiana, altered Chl and carotenoid pigment levels. MYB7 overexpression was associated with transcriptional activation of certain key genes involved in carotenoid biosynthesis, Chl biosynthesis, and other processes such as chloroplast and thylakoid membrane organization. Our results suggest that MYB7 plays a role in modulating carotenoid and Chl pigment accumulation in tissues through transcriptional activation of metabolic pathway genes.