Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.)

Planta ◽  
2021 ◽  
Vol 255 (1) ◽  
Author(s):  
Nosheen Kabir ◽  
Hai Lin ◽  
Xianhui Kong ◽  
Le Liu ◽  
Ghulam Qanmber ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Analysis ◽  
Functional Diversification

scholarly journals Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

2021 ◽  
Author(s):  
Yongxian Tian ◽  
Qigang Wang ◽  
Hao Zhang ◽  
Ningning Zhou ◽  
Huijun Yan ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Mlo Gene Family

scholarly journals Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

2019 ◽  
Vol 20 (22) ◽  
pp. 5796
Author(s):  
Qianqian Zhou ◽  
Qingchang Li ◽  
Peng Li ◽  
Songtao Zhang ◽  
Che Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Physiological Stress ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Hormone Treatment ◽  
Nicotiana Sylvestris ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Comprehensive Overview ◽  
Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

scholarly journals Evidence for Functional Diversification Within a Fungal NEP1-Like Protein Family

2013 ◽  
Vol 26 (3) ◽  
pp. 278-286 ◽  
Author(s):  
Parthasarathy Santhanam ◽  
H. Peter van Esse ◽  
Isabell Albert ◽  
Luigi Faino ◽  
Thorsten Nürnberger ◽  
...  
Keyword(s):  
Gene Family ◽  
Vegetative Growth ◽  
Nicotiana Benthamiana ◽  
Family Members ◽  
Aerial Mycelium ◽  
Vascular Wilt ◽  
In Planta ◽  
Functional Diversification ◽  
Targeted Deletion ◽  
Genes Encoding

In this study, we functionally analyzed the gene family encoding necrosis- and ethylene-inducing-like proteins (NLP) of the vascular wilt pathogen Verticillium dahliae. We show that the composition of the NLP gene family varies little among V. dahliae isolates. The cytotoxic activity of NLP family members of a tomato-pathogenic V. dahliae strain was determined, demonstrating that only two of the seven NLP induced plant cell death. The genes encoding these cytotoxic NLP were found to be induced in V. dahliae upon colonization of tomato. Interestingly, targeted deletion of either of the two genes in V. dahliae significantly compromised virulence on tomato as well as on Arabidopsis plants, whereas deletion of only one of the two genes affected virulence on Nicotiana benthamiana. This could be attributed to differential induction of the two NLP genes in V. dahliae upon N. benthamiana colonization, revealing that the in planta induction of NLP genes varies between plant hosts. Intriguingly, one of the NLP genes appears to also affect vegetative growth and conidiospore production, because the corresponding deletion strain produced significantly fewer conidiospores and developed extensive aerial mycelium. In conclusion, we demonstrate that the expanded V. dahliae NLP family shows functional diversification, revealing not only differential cytotoxicity between family members but also that the cytotoxic NLP play a role in vegetative growth and asexual reproduction in addition to their contribution to virulence.

scholarly journals Evolutionary expansion and functional diversification of oligopeptide transporter gene family in rice

Rice ◽  
2012 ◽  
Vol 5 (1) ◽  
pp. 12 ◽  
Author(s):  
Tao Liu ◽  
Jiqing Zeng ◽  
Kuaifei Xia ◽  
Tian Fan ◽  
Yuge Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Transporter Gene ◽  
Functional Diversification ◽  
Oligopeptide Transporter

scholarly journals Functional diversification of the dehydrin gene family in apple and its contribution to cold acclimation during dormancy

2015 ◽  
Vol 155 (3) ◽  
pp. 315-329 ◽  
Author(s):  
Vítor da Silveira Falavigna ◽  
Yohanna Evelyn Miotto ◽  
Diogo Denardi Porto ◽  
Rafael Anzanello ◽  
Henrique Pessoa dos Santos ◽  
...  
Keyword(s):  
Gene Family ◽  
Cold Acclimation ◽  
Functional Diversification ◽  
Dehydrin Gene

scholarly journals Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

2016 ◽  
Vol 29 (12) ◽  
pp. 950-964 ◽  
Author(s):  
Md Shakhawat Hossain ◽  
Arina Shrestha ◽  
Sihui Zhong ◽  
Mandana Miri ◽  
Ryan S. Austin ◽  
...  
Keyword(s):  
Gene Family ◽  
Lotus Japonicus ◽  
Cortical Cell ◽  
Plant Evolution ◽  
Nodule Formation ◽  
Functional Diversification ◽  
Nuclear Factor Y ◽  
Functional Analyses ◽  
Transcription Factor Gene Family ◽  
Selection Of

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

scholarly journals SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 354
Author(s):  
Shaokun Li ◽  
Li Li ◽  
Yang Jiang ◽  
Jun Wu ◽  
Honghua Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Panax Ginseng ◽  
Interaction Analysis ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Expression Characteristics ◽  
Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

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