A genome-wide analysis of genes and gene families involved in innate immunity of Bombyx mori

2008 ◽  
Vol 38 (12) ◽  
pp. 1087-1110 ◽  
Author(s):  
Hiromitsu Tanaka ◽  
Jun Ishibashi ◽  
Kosuke Fujita ◽  
Yoshiro Nakajima ◽  
Aki Sagisaka ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Bombyx Mori ◽  
Gene Families ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2019 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Wen-Wu Guo
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
In Vitro Regeneration ◽  
Gene Families ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few of B3 transcription factors are reported to regulate embryogenesis, little is known about the possible roles of B3 superfamily during SE especially in citrus. Results In this study, a total of 72 (CsB3) and 69 (CgB3) putative B3 superfamily members were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively, each comprised four gene families and 14 phylogenetic classes. The B3 genes were unevenly distributed over citrus chromosomes and other non-anchored scaffolds. Genome duplication analysis indicated that the segmental and tandem duplication events have significantly contributed to the expansion of the citrus B3 superfamily. The evolutionary relationships among the B3 family members and their putative functions were deduced based on the results of phylogenetic analysis. Furthermore, transcriptomic analysis showed that citrus B3 genes have differential expression levels in various tissues, suggesting distinct biological roles of different members. Expression analysis revealed that the B3 superfamily members showed four types of expression profiles during SE in citrus and may play functional roles during SE, especially at late SE stages. Of them, CsARF19 is specifically expressed in sweet orange and at markedly higher levels in the embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions This study provides a genome-wide analysis of citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, which contributes to a better understanding of the B3 genes in citrus and their association with SE.

scholarly journals Energetic Evolution of Cellular Transportomes

2017 ◽  
Author(s):  
Behrooz Darbani ◽  
Douglas B. Kell ◽  
Irina Borodina
Keyword(s):  
Ion Channels ◽  
Bacterial Species ◽  
Living Cells ◽  
Energetic Efficiency ◽  
Cellular Functions ◽  
Transporter Proteins ◽  
Genome Wide Analysis ◽  
Solute Carriers ◽  
Genome Wide ◽  
A Genome

ABSTRACTTransporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals A Genome‐Wide Analysis of Placental Epigenetic Markers in Response to Maternal Choline Supplementation

2017 ◽  
Vol 31 (S1) ◽  
Author(s):  
Sze Ting (Cecilia) Kwan ◽  
Minghui Wang ◽  
Julia H King ◽  
Jian Yan ◽  
Xinyin Jiang ◽  
...  
Keyword(s):  
Epigenetic Markers ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome
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