Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses.
The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. OnePeTIFYbelongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins ofArabidopsisandOryza sativaindicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship betweenP. edulis,O. sativa, andB. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication ofPeTIFYmay have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among theP. edulis-O. sativa,P. edulis-B. distachyon,andO. sativa-B. distachyonwas approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% ofPeTIFYgenes could be up-regulated by cold and dehydration stresses, and somePeTIFYsalso share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress.
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Zhuo
Z
Huang
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Si-Han
SH
Jin
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Han-Du
HD
Guo
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Xiao-Juan
XJ
Zhong
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Jiao
J
He
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Xi
X
Li
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Ming-Yan
MY
Jiang
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Xiao-Fang
XF
Yu
Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
Hai
H
Long
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Ming-Dong
MD
Ma
College of Landscape Architecture, Sichuan Agricultural University , Wenjiang , Sichuan , China.
Qi-Bing
QB
Chen
Cold stress; Dehydration; Gene family; Moso bammboo (Phyllostachys edulis); TIFY protein; Transcriptome sequencing