Gene loss in plants: Evidence from genome-wide phylogenetic analysis of thiamine pyrophosphate-dependent enzymes

2014 ◽  
Vol 53 (3) ◽  
pp. 221-227
Author(s):  
Xin-Min Tian ◽  
Peng Wang ◽  
Wen-Bin Hu ◽  
Da-Hai Gao ◽  
Qiong Li
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Thiamine Pyrophosphate ◽  
Genome Wide

scholarly journals A novel phyllosphere residentProtomycesspecies that interacts with theArabidopsisimmune system

2019 ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
Pia Laine ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Signalling Pathways ◽  
Alternate Host ◽  
Single Strain ◽  
Genomic Changes ◽  
Gene Retention ◽  
Genome Wide ◽  
Host Jump

ABSTRACTWe describe the genome contents of sixProtomycesspp. that are pathogenic within the typical host range of the genus and a novelProtomycesstrain (SC29) that was previously isolated from the phylloplane of wildArabidopsis thaliana(Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinctProtomycessp. Analysis of gene family expansions, gene retention, and gene loss patterns among theseProtomycesspp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle ofProtomycesspp. was previously unknown. Genomic changes in SC29 and all otherProtomycesspp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease onArabidopsisas a single strain, but could persist in its phylloplane, while the closely relatedP. inouyeidoes not. SC29 treatedArabidopsisexhibited enhanced immunity againstBotrytis cinereainfection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novelProtomycessp. able to survive in theArabidopsisphylloplane and that phylloplane residency is an important element in the lifecycle ofProtomycesspp.

scholarly journals In silico genome-wide identification and phylogenetic analysis of the WRKY transcription factor family in sweet orange (Citrus sinensis)

2017 ◽  
Vol 11 (06) ◽  
pp. 716-726 ◽  
Author(s):  
Eduardo Goiano da Silva ◽  
◽  
Tania Mayumi Ito ◽  
Silvia Graciele Hülse de Souza ◽  
◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factor ◽  
In Silico ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Wrky Transcription Factor ◽  
Transcription Factor Family ◽  
Genome Wide

Genome-wide Identification, Phylogenetic Analysis, and Expression Profiling of CONSTANS-like (COL) Genes in Vitis vinifera

2018 ◽  
Vol 38 (2) ◽  
pp. 631-643 ◽  
Author(s):  
Ling Wang ◽  
Jingyi Xue ◽  
Weina Dai ◽  
Yujin Tang ◽  
Peijie Gong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vitis Vinifera ◽  
Expression Profiling ◽  
Genome Wide

scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1430
Author(s):  
Yuanfeng Xu ◽  
Jinbin Zheng ◽  
Yanan Yang ◽  
Zhaoxia Cui
Keyword(s):  
Phylogenetic Analysis ◽  
Environmental Stress ◽  
Tandem Duplication ◽  
High Salinity ◽  
Expression Profiles ◽  
Eriocheir Sinensis ◽  
Biological Processes ◽  
Synteny Analysis ◽  
Air Exposure ◽  
Genome Wide

DDE transposase 4 (DDE_Tnp_4) family is a large endonuclease family involved in a wide variety of biological processes. However, little information is available about this family in crustaceans. In this study, we used HMMER to identify 39 DDE_Tnp_4 family genes in Eriocheir sinensis genome, and the genes were classified into four subfamilies according to phylogenetic analysis. Gene expansions occurred among E. sinensis genome, and synteny analysis revealed that some DDE_Tnp_4 family genes were caused by tandem duplication. In addition, the expression profiles of DDE_Tnp_4 family genes in E. sinensis indicated that subfamily I and II genes were up-regulated in response to acute high salinity and air exposure stress. E. sinensis is a kind of economical crustacean with strong tolerance to environmental stress. We confirmed the expansion of DDE_Tnp_4 family genes in E. sinensis and speculated that this expansion is associated with strong tolerance of E. sinensis. This study sheds light on characterizations and expression profiles of DDE_Tnp_4 family genes in E. sinensis and provides an integrated framework for further investigation on environmental adaptive functions of DDE_Tnp_4 family in crustaceans.

scholarly journals Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing Solanum commersonii

Life ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 37
Author(s):  
Clizia Villano ◽  
Vincenzo D’Amelia ◽  
Salvatore Esposito ◽  
Maria Grazia Adelfi ◽  
Felice Contaldi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Segmental Duplications ◽  
Solanum Commersonii ◽  
Abiotic Stressors ◽  
Genome Wide ◽  
Specific Manner ◽  
Plant Families ◽  
Coa Reductase ◽  
Specific Pathway ◽  
Family Investigation

Steroidal glycoalkaloids (SGAs) are a class of nitrogen-containing glycosides occurring in several plant families and biosynthesized through a specific pathway. HMG-CoA reductase is the first enzyme of this pathway, and its transcription can be regulated by biotic and abiotic stressors and even in a tissue-specific manner. This study aimed to characterize the HMG genes family in a tuber-bearing potato species, Solanum commersonii, using transcriptional and functional approaches. Our results provided evidence that four ScHMGs with different tissue-specificities represent the HMG gene family in S. commersonii and that they originated from ScHMG1 through segmental duplications. Phylogenetic analysis suggests that ScHMG1 is the direct ortholog of AtHMG1, which is associated with SGAs accumulation in plants. Its overexpression in S. commersonii revealed that this gene plays a key role in the accumulation of glycoalkaloids regulating the production of dehydrocommersonine.

Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes

2014 ◽  
Vol 75 ◽  
pp. 154-164 ◽  
Author(s):  
Xiao-Yang Zhi ◽  
Ji-Cheng Yao ◽  
Hong-Wei Li ◽  
Ying Huang ◽  
Wen-Jun Li
Keyword(s):  
Phylogenetic Analysis ◽  
Shikimate Pathway ◽  
Early Evolution ◽  
Genome Wide

scholarly journals Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum)

PLoS ONE ◽  
2020 ◽  
Vol 15 (7) ◽  
pp. e0236454 ◽  
Author(s):  
Essa Ali ◽  
Mohammad Ammar Raza ◽  
Ming Cai ◽  
Nazim Hussain ◽  
Ahmad Naeem Shahzad ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Linum Usitatissimum ◽  
Transcription Activator ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
Genome Wide Survey

scholarly journals Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

2003 ◽  
Vol 14 (1) ◽  
pp. 29-36 ◽  
Author(s):  
Y. I. Wolf
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Wide

Genome wide identification of taste receptor genes in common carp (Cyprinus carpio) and phylogenetic analysis in teleost

Gene ◽  
2018 ◽  
Vol 678 ◽  
pp. 65-72 ◽  
Author(s):  
Shengnan Kong ◽  
Chuanju Dong ◽  
Hongzao Lv ◽  
Lin Chen ◽  
Jiangfan Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Taste Receptor ◽  
Common Carp Cyprinus Carpio ◽  
Genome Wide ◽  
Carp Cyprinus Carpio
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