scholarly journals Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2620 ◽  
Author(s):  
Zhuo Huang ◽  
Si-Han Jin ◽  
Han-Du Guo ◽  
Xiao-Juan Zhong ◽  
Jiao He ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stress Tolerance ◽  
Divergence Time ◽  
Purifying Selection ◽  
Moso Bamboo ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
Phyllostachys Edulis ◽  
Genome Wide

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.

scholarly journals Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

2019 ◽  
Vol 20 (17) ◽  
pp. 4309 ◽  
Author(s):  
Ruihua Wu ◽  
Yanrong Shi ◽  
Qian Zhang ◽  
Wenqing Zheng ◽  
Shaoliang Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Divergence Time ◽  
Duplication Event ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Evolutionary Patterns ◽  
Genome Wide ◽  
Comparative Phylogenetic Analysis

The largest group of deubiquitinases—ubiquitin-specific proteases (UBPs)—perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.

Genome-Wide Identification of Trihelix Genes in Moso Bamboo (Phyllostachys edulis) and Their Expression in Response to Abiotic Stress

2019 ◽  
Vol 38 (3) ◽  
pp. 1127-1140
Author(s):  
Hongyan Gao ◽  
Rong Huang ◽  
Jun Liu ◽  
Zhimin Gao ◽  
Hansheng Zhao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Genome Wide

scholarly journals Correction to: Genome-wide Identification of Trihelix Genes in Moso Bamboo (Phyllostachys edulis) and Their Expression in Response to Abiotic Stress

2019 ◽  
Vol 38 (4) ◽  
pp. 1616-1616 ◽  
Author(s):  
Hongyan Gao ◽  
Rong Huang ◽  
Jun Liu ◽  
Zhimin Gao ◽  
Hansheng Zhao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Genome Wide

scholarly journals Genome-Wide Identification and Characterization of Hexokinase Genes in Moso Bamboo (Phyllostachys edulis)

2020 ◽  
Vol 11 ◽  
Author(s):  
Wenqing Zheng ◽  
Yuan Zhang ◽  
Qian Zhang ◽  
Ruihua Wu ◽  
Xinwei Wang ◽  
...  
Keyword(s):  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Genome Wide ◽  
Identification And Characterization

scholarly journals Overexpression of PheNAC3 from moso bamboo promotes leaf senescence and enhances abiotic stress tolerance in Arabidopsis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8716
Author(s):  
Lihua Xie ◽  
Miaomiao Cai ◽  
Xiangyu Li ◽  
Huifang Zheng ◽  
Yali Xie ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Leaf Senescence ◽  
Stress Responses ◽  
Abiotic Stress Tolerance ◽  
Moso Bamboo ◽  
Biotic And Abiotic Stress ◽  
Phyllostachys Edulis ◽  
Salt And Drought Stress ◽  
Nac Family

The NAC family is one of the largest transcription factor families unique to plants, which regulates the growth and development, biotic and abiotic stress responses, and maturation and senescence in plants. In this study, PheNAC3, a NAC gene, was isolated and characterized from moso bamboo (Phyllostachys edulis). PheNAC3 belong to the NAC1 subgroup and has a conserved NAC domain on the N-terminus, which with 88.74% similarity to ONAC011 protein. PheNAC3 localized in the nucleus and exhibited transactivation activity. PheNAC3 was upregulated during the process of senescence of leaves and detected shoots. PheNAC3 was also induced by ABA, MeJA, NaCl and darkness, but it had no remarkable response to PEG and SA treatments. Overexpression of PheNAC3 could cause precocious senescence in Arabidopsis. Transgenic Arabidopsis displayed faster seed germination, better seedling growth, and a higher survival rate than the wild-type under salt or drought stress conditions. Moreover, AtSAG12 associated with senescence and AtRD29A and AtRD29b related to ABA were upregulated by PheNAC3 overexpression, but AtCAB was inhibited. These findings show that PheNAC3 may participate in leaf senescence and play critical roles in the salt and drought stress response.

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

2021 ◽  
Author(s):  
Pooja Moni Baruah ◽  
Debasish B. Krishnatreya ◽  
Kuntala Sarma Bordoloi ◽  
Sarvajeet Singh Gill ◽  
Niraj Agarwala
Keyword(s):  
Abiotic Stress ◽  
Capsicum Annuum ◽  
Genome Wide ◽  
Identification And Characterization

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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