scholarly journals Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family in Potato (Solanum tuberosum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Xuanshong Yang ◽  
Jiazheng Yuan ◽  
Wenbin Luo ◽  
Mingyue Qin ◽  
Jiahan Yang ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Solanum Tuberosum L ◽  
Pcr Analysis ◽  
Class Iii ◽  
Protein Motifs ◽  
Real Time Quantitative Pcr ◽  
Gene Pairs ◽  
Genome Wide ◽  
Class Iii Peroxidases

Class III peroxidases (PRXs) are plant-specific enzymes and play important roles in plant growth, development and stress response. In this study, a total of 102 non-redundant PRX gene members (StPRXs) were identified in potato (Solanum tuberosum L.). They were divided into 9 subfamilies based on phylogenetic analysis. The members of each subfamily were found to contain similar organizations of the exon/intron structures and protein motifs. The StPRX genes were not equally distributed among chromosomes. There were 57 gene pairs of segmental duplication and 26 gene pairs of tandem duplication. Expression pattern analysis based on the RNA-seq data of potato from public databases indicated that StPRX genes were expressed differently in various tissues and responded specifically to heat, salt and drought stresses. Most of the StPRX genes were expressed at significantly higher levels in root than in other tissues. In addition, real-time quantitative PCR (qRT-PCR) analysis for 7 selected StPRX genes indicated that these genes displayed various expression levels under abiotic stresses. Our results provide valuable information for better understanding the evolution of StPRX gene family in potato and lay the vital foundation for further exploration of PRX gene function in plants.

scholarly journals MYB Gene Family in Potato (Solanum tuberosum L.): Genome-Wide Identification of Hormone-Responsive Reveals Their Potential Functions in Growth and Development

2019 ◽  
Vol 20 (19) ◽  
pp. 4847 ◽  
Author(s):  
Wenjun Sun ◽  
Zhaotang Ma ◽  
Hui Chen ◽  
Moyang Liu
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Solanum Tuberosum L ◽  
Potential Functions ◽  
Anthocyanin Synthesis ◽  
Myb Gene ◽  
Genome Wide ◽  
R2r3 Myb

As an important nongrain crop, the growth and yield of potato (Solanum tuberosum L.) is often affected by an unfavorable external environment in the process of cultivation. The MYB family is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. Several MYB genes in potato that regulate anthocyanin synthesis and participate in abiotic stress responses have been identified. To identify all Solanum tuberosum L. MYB (StMYB) genes involved in hormone or stress responses to potentially regulate potato growth and development, we identified the MYB gene family at the genome-wide level. In this work, 158 StMYB genes were found in the potato genome. According to the amino acid sequence of the MYB domain and gene structure, the StMYB genes were divided into R2R3-MYB and R1R2R3-MYB families, and the R2R3-MYB family was divided into 20 subgroups (SGs). The expression of 21 StMYB genes from different SGs in roots, stems, leaves, flowers, shoots, stolons, young tubers, and mature tubers was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression patterns of StMYB genes in potatoes treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin acid 3 (GA3), NaCl, mannitol, and heat were also measured. We have identified several potential candidate genes that regulate the synthesis of potato flavonoids or participate in hormone or stress responses. This work provides a comprehensive understanding of the MYB family in potato and will lay a foundation for the future investigation of the potential functions of StMYB genes in the growth and development of potato.

scholarly journals CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Potato (Solanum tuberosum L.): Identification and Expression Analysis

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 984
Author(s):  
Maria Gancheva ◽  
Irina Dodueva ◽  
Maria Lebedeva ◽  
Ludmila Lutova
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Solanum Tuberosum L ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Regulatory Sequences ◽  
Functional Studies ◽  
Cle Peptides ◽  
Using Data ◽  
Potato Growth

CLE genes encode a group of small secretory peptides, which regulate cell proliferation and differentiation in plants. CLE genes have been studied in many plants; however, little is known about this gene family in potato. In this study, we characterized members of the CLE gene family in potato Solanum tuberosum (StCLE) and comprehensively analyzed their phylogenetic relationships, structure, and expression patterns. Using available transcriptomic data, we found a relative high expression level of StCLE8, StCLE12, and StCLE13 in stolons and tubers. Real-time PCR analysis showed that the StCLE23 gene was upregulated by water deficiency, whereas the expression of StCLE4 and StCLE10 was induced by nitrogen supply. Besides that, using data from transcriptomic studies obtained previously for plants with the induction the StBEL5 gene, a positive regulator of tuber development, we found that StCLE4 was among genes upregulated in response to StBEL5 induction, suggesting that StCLE4 could be a target of StBEL5 transcription factor. However, we did not reveal a direct binding of StBEL5 to the regulatory sequences of StCLE4 using yeast one-hybrid assay. Taken together, our data provide basic information for future functional studies of CLE peptides in potato growth and tuberization and in response to various environmental stimuli.

Genome-wide identification and analysis of the aldehyde dehydrogenase gene superfamily in Chinese cabbage (Brassica rapa subsp. pekinensis)

2019 ◽  
Vol 99 (4) ◽  
pp. 420-436 ◽  
Author(s):  
Xin Jiang ◽  
Jie Ren ◽  
Xueling Ye ◽  
Mingfeng Liu ◽  
Qingqing Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Chinese Cabbage ◽  
Growth And Development ◽  
Chromosomal Mapping ◽  
Protein Motifs ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
Dehydrogenase Gene ◽  
Different Tissues ◽  
Aldh Gene

Aldehyde dehydrogenases (ALDHs) encode a class of enzymes that dehydrooxidize aldehydes into corresponding carboxylic acids, which are involved in the growth and development of plants and in the response to various biological and abiotic stresses. In this study, we identified 27 ALDH genes in the Chinese cabbage genome and grouped them into 10 different families. Chromosomal mapping revealed that, except for one gene distributed on Scaffold, the remaining 26 genes were unevenly distributed on 10 chromosomes of Chinese cabbage. Based on a comparison of the homologous relationship between BrALDHs and ALDH genes in Arabidopsis thaliana, duplicated patterns of the ALDH gene family in Chinese cabbage were analyzed. The exon–intron structures, conserved protein motifs, and phylogenetic relationship with ALDH in six other species were also predicted and analyzed. Finally, we used available RNA-Seq data and real-time quantitative PCR to analyze the expression of ALDH genes in different tissues of Chinese cabbage including the roots, stems, leaves, flowers, and siliques. The results showed the tissue specificity and differential expression in different tissues of BrALDHs. The analysis of ALDH gene transcriptome data of Chinese cabbage under different stress conditions (cold, heat, drought, and salinity) showed that the response levels of different genes varied under different stresses, suggesting the function of some genes in these processes. Details of the ALDH gene family in Chinese cabbage has enriched studies on the ALDH gene family in plants and animals and is crucial for understanding ALDH function during plant growth and development.

Genome-wide identification, phylogeny and expression profiling of class III peroxidases gene family in Brachypodium distachyon

Gene ◽  
2019 ◽  
Vol 700 ◽  
pp. 149-162 ◽  
Author(s):  
Ting Zhu ◽  
Fang Xin ◽  
ShuWei Wei ◽  
Yue Liu ◽  
YuCui Han ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Brachypodium Distachyon ◽  
Class Iii ◽  
Genome Wide ◽  
Class Iii Peroxidases

Genome-wide identification and analysis of the Q-type C2H2 gene family in potato (Solanum tuberosum L.)

2020 ◽  
Vol 153 ◽  
pp. 327-340
Author(s):  
Zhen Liu ◽  
Jeffrey A. Coulter ◽  
Yuanming Li ◽  
Xiaojing Zhang ◽  
Jiangang Meng ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Solanum Tuberosum L ◽  
Genome Wide

scholarly journals Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9310 ◽  
Author(s):  
Weina Zhang ◽  
Zhongjian Chen ◽  
Yichen Kang ◽  
Yanling Fan ◽  
Yuhui Liu ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Family Members ◽  
Pcr Analysis ◽  
Chromosomal Distribution ◽  
Potato Genome ◽  
Lectin Receptor ◽  
Genome Wide ◽  
The Family ◽  
Duplication Events

Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.

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