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 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.

Protohemiphlebiidae fam. nov., a stem hemiphlebioid damselfly from Cretaceous amber in Kachin

2021 ◽  
pp. SP521-2020-249
Author(s):  
Daran Zheng ◽  
Edmund A. Jarzembowski ◽  
De Zhuo ◽  
André Nel
Keyword(s):  
Phylogenetic Analysis ◽  
Late Jurassic ◽  
New Genus ◽  
Early Evolution ◽  
Relict Species ◽  
Wing Base ◽  
New Family ◽  
Stem Group ◽  
The Family

AbstractHemiphlebiidae are the most basal lestomorphan family following the latest phylogenetic analysis of the Zygoptera: this unique damselfly family today contains one relict species found in the wetlands of Australia. It was, however, very diverse and widespread during the Mesozoic. Nevertheless, very few species were known obscuring the origination and early evolution of the family. Here we propose a new stem hemiphlebioid taxon (Protohemiphlebiidae Zheng, Jarzembowski & Nel, fam. nov.) based on a new genus and two species: Protohemiphlebia zhangi Zheng, Jarzembowski & Nel, sp. nov. and Protohemiphlebia meiyingae Zheng, Jarzembowski & Nel, sp. nov. The new family shares the characters of both Hemiphlebiidae and Coenagrionoidea, but it is more closely related to Hemiphlebiidae in having the pterostigma with a ‘star-shaped’ microsculpture, and AA originating from the wing base slightly distal of Ax0. Protohemiphlebia Zheng, Jarzembowski & Nel, gen. nov. is further considered to belong to the stem group of Hemiphlebioidea, instead of belonging to the Hemiphlebiidae, in possessing pretibial combs and a weakly kinked RP1 below the Pt-brace. The new damselflies will help to calibrate the origin of Hemiphlebiidae, which could be earlier than their current oldest records in the Kimmeridgean (Late Jurassic).

scholarly journals Jaw elements in Plumulites bengtsoni confirm that machaeridians are extinct armoured scaleworms

2019 ◽  
Vol 286 (1907) ◽  
pp. 20191247 ◽  
Author(s):  
Luke A. Parry ◽  
Gregory D. Edgecombe ◽  
Dan Sykes ◽  
Jakob Vinther
Keyword(s):  
Phylogenetic Analysis ◽  
Early Evolution ◽  
The Body ◽  
Common Origin ◽  
Discrete Elements ◽  
Crown Group ◽  
Total Group ◽  
Early Ordovician ◽  
Jaw Apparatus ◽  
Competing Hypotheses

Machaeridians are Palaeozoic animals that are dorsally armoured with serialized, imbricating shell plates that cover or enclose the body. Prior to the discovery of an articulated plumulitid machaeridian from the Early Ordovician of Morocco that preserved unambiguous annelid characters (segmental parapodia with chaetae), machaeridians were a palaeontological mystery, having been previously linked to echinoderms, barnacles, tommotiids (putative stem-group brachiopods) or molluscs. Although the annelid affinities of machaeridians are now firmly established, their position within the phylum and relevance for understanding the early evolution of Annelida is less secure, with competing hypotheses placing Machaeridia in the stem or deeply nested within the crown group of annelids. We describe a scleritome of Plumulites bengtsoni from the Fezouata Formation of Morocco that preserves an anterior jaw apparatus consisting of at least two discrete elements that exhibit growth lines. Although jaws have multiple independent origins within the annelid crown group, comparable jaws are present only within Phyllodocida, the clade that contains modern aphroditiforms (scaleworms and relatives). Phylogenetic analysis places a monophyletic Machaeridia within the crown group of Phyllodocida in total-group Aphroditiformia, consistent with a common origin of machaeridian shell plates and scaleworm elytrae. The inclusion of machaeridians in Aphroditiformia truncates the ghost lineage of Phyllodocida by almost a hundred million years.

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.

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 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
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