SOM encodes a nucleus-localized CCCH-type zinc finger protein and negatively regulates seed germination in Arabidopsis thaliana. We have previously demonstrated that ectopic expression of Sl ABI3, an important transcription factor in abscisic acid(ABA) signaling pathway, resulted in alteration of Sl SOM expression patterns in both leaf and seed of tomato. In this study, we aimed to elucidate the function of tomato Sl SOM in regarding to seed germination and seedling development. Here, we constructed Sl SOM over-expression vector p BI121-SOM driven by Ca MV 35 S promoter, and the recombinant plasmid was incorporated into wild-type tomato by the method of Agrobacterium tumefaciens-mediated transformation. The result showed that over-expression of Sl SOM conferred enhanced responses to exogenous ABA application during seed germination and seedling development. In addition, ectopic expression of Sl SOM resulted in the alteration of expression level of ABA/GA(gibberellins) metabolic genes, such as Sl ABA1, Sl CYP707A1, Sl GA3ox2, and Sl GA2ox4, in both leaf and seed. The ABA anabolic gene Sl ABA1 and the GA catabolic gene Sl GA2ox4 were up-regulated while the ABA catabolic gene Sl CYP707A1 and the GA anabolic gene Sl GA3ox2 were down-regulated. Compared to wild type, the expression level of Sl ABI5 was increased by about 40–50% in transgenic seeds while adding exogenous ABA treatment. These results support the notion that Sl SOM inhibits seed germination by regulating ABA/GA metabolic genes and Sl ABI5 expression in Solanum lycopersicum.
SUN Xiao-chunGAO Yong-fengZHANG NingLI Hui-rongYANG Shu-zhangLIU Yong-sheng
In several stress responsive gene loci of monocot cereal crops,we have previously identified an unusual posttranscriptional processing mediated by paired presence of short direct repeated (SDR) sequences at 5' and 3' splicing junctions that are distinct from conventional (U2/U12-type) splicing boundaries.By using the known SDR-containing sequences as probes,24 plant candidate genes involved in diverse functional pathways from both monocots and dicots that potentially possess SDR-mediated posttranscriptional processing were predicted in the GenBank database.The SDRs-mediated posttranscriptional processing events including cis-and trans-actions were experimentally detected in majority of the predicted candidates.Extensive sequence analysis demonstrates several types of SDR-associated splicing peculiarities including partial exon deletion,exon fragment repetition,exon fragment scrambling and trans-splicing that result in either loss of partial exon or unusual exonic sequence rearrangements within or between RNA molecules.In addition,we show that the paired presence of SDR is necessary but not sufficient in SDR-mediated splicing in transient expression and stable transformation systems.We also show prokaryote is incapable of SDR-mediated premRNA splicing.
Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.
Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C contents.Since the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.To efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://kiwifruitgenome.org/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search tool.Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis.
