Whole transcriptome sequencing reveals genes involved in plastid/chloroplast division and development are regulated by the HP1/DDB1 at an early stage of tomato fruit development.
The phenotype of tomato high pigment-1 (hp1) mutant is characterized by overproduction of pigments including chlorophyll and carotenoids during fruit development and ripening. Although the increased plastid compartment size has been thought to largely attribute to the enhanced pigmentation, the molecular aspects of how the HP1/DDB1 gene manipulates plastid biogenesis and development are largely unknown. In the present study, we compared transcriptome profiles of immature fruit pericarp tissue between tomato cv. Ailsa Craig (WT) and its isogenic hp1 mutant. Over 20 million sequence reads, representing > 1.6 Gb sequence data per sample, were generated and assembled into 21,972 and 22,167 gene models in WT and hp1, respectively, accounting for over 60 % official gene models in both samples. Subsequent analyses revealed that 8,322 and 7,989 alternative splicing events, 8833 or 8510 extended 5'-UTRs, 8,263 or 8,939 extended 3'-UTRs, and 1,136 and 1,133 novel transcripts, exist in WT and hp1, respectively. Significant differences in expression level of 880 genes were detected between the WT and hp1, many of which are involved in signaling transduction, transcription regulation and biotic and abiotic stresses response. Distinctly, RNA-seq datasets, quantitative RT-PCR analyses demonstrate that, in hp1 mutant pericarp tissue at early developmental stage, an apparent expression alteration was found in several regulators directly involved in plastid division and development. These results provide a useful reference for a more accurate and more detailed characterization of the molecular process in the development and pigmentation of tomato fruits.
Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
Xiaofeng
X
Tang
Zizhi
Z
Tang
Shengxiong
S
Huang
Jikai
J
Liu
Jia
J
Liu
Wei
W
Shi
Xuefen
X
Tian
Yuxiang
Y
Li
Danfeng
D
Zhang
Jian
J
Yang
Yongfeng
Y
Gao
Deer
D
Zeng
Pei
P
Hou
Xiangli
X
Niu
Ying
Y
Cao
Guangwei
G
Li
Xiao
X
Li
Fangming
F
Xiao
Yongsheng
Y
Liu
D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D017398:Alternative Splicing / Q000235:genetics; D005638:Fruit / Q000235:genetics / Q000254:growth & development*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development*; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018087:Plastids / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D010940:Plant Proteins; D012333:RNA, Messenger