scholarly journals Genome-Wide Identification of Chalcone Reductase Gene Family in Soybean: Insight into Root-Specific GmCHRs and Phytophthora sojae Resistance

2017 ◽  
Vol 8 ◽  
Author(s):  
Caroline J. Sepiol ◽  
Jaeju Yu ◽  
Sangeeta Dhaubhadel
Keyword(s):  
Gene Family ◽  
Phytophthora Sojae ◽  
Genome Wide ◽  
Reductase Gene ◽  
Chalcone Reductase ◽  
Insight Into

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals In-silico genome-wide identification and characterisation of NBS-LRR gene family in banana Musa acuminata

2021 ◽  
Vol 63 (12) ◽  
pp. 52-58
Author(s):  
Duc Trung Tran ◽  
◽  
Hong Linh Ta ◽  
Keyword(s):  
Gene Family ◽  
Musa Acuminata ◽  
Functional Evaluation ◽  
Practical Application ◽  
Resistant Genes ◽  
Intensive Exploitation ◽  
Genome Wide ◽  
Potential Resource ◽  
Cultivation Techniques ◽  
Insight Into

Various common diseases caused by bacteria and viruses are increasing threats to the production of bananas worldwide. Besides the practical application of cultivation techniques, intensive exploitation of resistant genes, most of which belong to the NBS-LRR(Nucleotide-binding site - Leucine-rich repeat) gene family, in fortifying banana’s disease resistance, has been considered as a sustainable approach. The recently published genome assembly of Musa acuminata, a species of the Musa genus native to Southern Asia, has facilitated the genome-wide identification and characterisation of NBS-LRR genes. In the present study, an in-silicoapproach was employed to identify and characterise 97 NBS-LRR genes and their evolution in M. acuminatagenome. Except Ma_NBS_083 belonging to the RNLsub-family, other identified genes are members of the sub-family CNL and most of them contain only one exon. Sixty-six (66) NBS-LRR genes (68%) were mapped on 11 banana chromosomes, among them 38 genes (39%) located in clusters. Phylogenetic analysis in combination with conserved motif identification classified the banana NBS-LRR genes into seven groups. This study provides novel insight into the NBS-LRR gene family in bananas as a potential resource for further research in functional evaluation and utilisation of resistant genes.

scholarly journals Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinzi Yu ◽  
Zhaolan Mo ◽  
Xianghai Tang ◽  
Tian Gao ◽  
Yunxiang Mao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dehydration Stress ◽  
Pyropia Yezoensis ◽  
Genome Wide ◽  
Regulated Expression ◽  
Relative Conservation ◽  
Shock Proteins ◽  
Insight Into

Abstract Background Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis. Results We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution. Conclusions These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.

scholarly journals Genome-Wide Analysis of NAC Gene Family in Betula pendula

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 741 ◽  
Author(s):  
Song Chen ◽  
Xin Lin ◽  
Dawei Zhang ◽  
Qi Li ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Betula Pendula ◽  
Low Temperature Stress ◽  
Specific Expression ◽  
Genome Wide ◽  
Nac Gene Family ◽  
Cold Responses ◽  
Insight Into

NACs (NAM, ATAF1/2, and CUC2) are plant-specific transcription factors that play diverse roles in various plant developmental processes. In this study, we identified the NAC gene family in birch (Betula pendula) and further analyzed the function of BpNACs. Phylogenetic analysis reveals that the 114 BpNACs can be divided into seven subfamilies. We investigated the expression levels of these BpNACs in different tissues of birch including roots, xylem, leaves, and flowers, and the results showed that the BpNACs seem to be expressed higher in xylem and roots than leaves and flowers. In addition to tissue-specific expression analysis, we investigated the expression of BpNACs under low-temperature stress. A total of 21 BpNACs were differentially expressed under low-temperature stress, of which 17 were up-regulated, and four were down-regulated. Using the gene expression data, we reconstructed the gene co-expression network for the 21 low-temperature-responsive BpNACs. In conclusion, our results provide insight into the evolution of NAC genes in the B. pendula genome, and provide a basis for understanding the molecular mechanism for BpNAC-mediated cold responses in birch.

Genome-wide identification and analysis of maize PAL gene family and its expression profile in response to high-temperature stress

2020 ◽  
Vol 52 (5) ◽  
Author(s):  
De-Gong Wu ◽  
Qiu-Wen Zhan ◽  
Hai-Bing Yu ◽  
Bao-Hong Huang ◽  
Xin-Xin Cheng ◽  
...  
Keyword(s):  
High Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Expression Profile ◽  
High Temperature Stress ◽  
Genome Wide

Genome-wide Analysis and Expression Profiling of SPS Gene Family in Brassica nupus L.

2018 ◽  
Vol 44 (2) ◽  
pp. 197
Author(s):  
Li ZHANG ◽  
Hong-Ju JIAN ◽  
Bo YANG ◽  
Ao-Xiang ZHANG ◽  
Chao ZHANG ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-Wide Identification, Classification, and Expression of NF-YB Gene Family in Soybean

2013 ◽  
Vol 38 (9) ◽  
pp. 1570-1582
Author(s):  
Wei-Jun ZHENG ◽  
Zhao-Shi XU ◽  
Zhi-Juan FENG ◽  
Lian-Cheng LI ◽  
Ming CHEN ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Wide
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