title: SRNAome parsing yields insights into tomato fruit ripening control.
abstract: Small RNAs have emerged as critical regulators in the expression and function of eukaryotic genomes at the post-transcriptional level. To elucidate the functions of microRNA (miRNAs) and endogenous small-interfering RNAs (siRNAs) in tomato fruit ripening process, the deep sequencing and bioinformatics methods were combined to parse the small RNAs landscape in three fruit-ripening stages (mature green, breaker and red-ripe) on a whole genome. Two species-specific miRNAs and two members of TAS3 family were identified, 590 putative phased small RNAs and 125 cis-natural antisense (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository and all of them showed differential expression patterns during fruit ripening. A large amount of the targets of the small RNAs were predicted to be involved in fruit ripening and ethylene pathway. Furthermore, the promoters of the conserved and novel miRNAs were found to contain the conserved motifs of TATA-box and CT microsatellites which were also found in Arabidopsis and rice, and several species-specific motifs were found in parallel.
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.|Laboratory of Postharvest Storage and Processing of Vegetables, National Engineering Research Center for Vegetables, Beijing, 100097, China.|Laboratory of Postharvest Storage and Processing of Vegetables, Vegetable Research Centre, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
authors.forename: Jinhua
authors.initials: J
authors.lastname: Zuo
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Daqi
authors.initials: D
authors.lastname: Fu
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Guiqin
authors.initials: G
authors.lastname: Qu
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Huiqin
authors.initials: H
authors.lastname: Tian
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Baiqiang
authors.initials: B
authors.lastname: Zhai
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Ju
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Gao
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Yunxiang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Yunbo
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Benzhong
authors.initials: B
authors.lastname: Zhu
mesh_terms: D001483:Base Sequence; D005030:Ethylenes / Q000378:metabolism*; D005638:Fruit / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D035683:MicroRNAs / Q000235:genetics*; D010937:Plant Growth Regulators / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005030:Ethylenes; D035683:MicroRNAs; D010937:Plant Growth Regulators; D018749:RNA, Plant; C036216:ethylene