Prediction of orthologous relationship by functionally important sites

2005 ◽  
Vol 78 (3) ◽  
pp. 209-222 ◽  
Author(s):  
Hsuan-Chao Chiu ◽  
C. Allen Chang ◽  
Yuh-Jyh Hu
Keyword(s):  
Orthologous Relationship

scholarly journals Identification and Expression Profiling of the BTB Domain-Containing Protein Gene Family in the Silkworm,Bombyx mori

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Daojun Cheng ◽  
Wenliang Qian ◽  
Meng Meng ◽  
Yonghu Wang ◽  
Jian Peng ◽  
...  
Keyword(s):  
Protein Gene ◽  
Domain Architecture ◽  
Gene Families ◽  
Monarch Butterfly ◽  
Duplication Event ◽  
Orthologous Relationship ◽  
Specific Expression ◽  
Protein Protein Interaction ◽  
Btb Domain ◽  
Silkworm Bombyx Mori

The BTB domain is a conserved protein-protein interaction motif. In this study, we identified 56 BTB domain-containing protein genes in the silkworm, in addition to 46 in the honey bee, 55 in the red flour beetle, and 53 in the monarch butterfly. Silkworm BTB protein genes were classified into nine subfamilies according to their domain architecture, and most of them could be mapped on the different chromosomes. Phylogenetic analysis suggests that silkworm BTB protein genes may have undergone a duplication event in three subfamilies: BTB-BACK-Kelch, BTB-BACK-PHR, and BTB-FLYWCH. Comparative analysis demonstrated that the orthologs of each of 13 BTB protein genes present a rigorous orthologous relationship in the silkworm and other surveyed insects, indicating conserved functions of these genes during insect evolution. Furthermore, several silkworm BTB protein genes exhibited sex-specific expression in larval tissues or at different stages during metamorphosis. These findings not only contribute to a better understanding of the evolution of insect BTB protein gene families but also provide a basis for further investigation of the functions of BTB protein genes in the silkworm.

scholarly journals Structural And Functional Analysis of CCT Family Genes In Pigeonpea

2021 ◽  
Author(s):  
Kishor U. Tribhuvan ◽  
Tanvi Kaila ◽  
Harsha Srivast ◽  
Antara Das ◽  
Kuldeep Kumar ◽  
...  
Keyword(s):  
Response Regulator ◽  
Variable Number ◽  
Photoperiod Response ◽  
Legume Species ◽  
Orthologous Relationship ◽  
Highly Sensitive ◽  
Pseudo Response Regulator ◽  
One And Many ◽  
Photoperiod Sensitive ◽  
Plausible Reason

Abstract Pigeonpea (Cajanus cajan (L) Millsp) is a short-day plant in which the flowering is highly sensitive to photoperiod. A better understanding of the genes modulating photoresponse and flowering time is critical to developing photoperiod insensitive pigeonpea cultivars for cultivation across the seasons. We identified 33 CCT family genes (CcCCT1- CcCCT33) in C. cajan and localized them on 10 chromosomes and nine genomic scaffolds. The structural analysis of CCT family genes revealed a considerable variation in length and distribution of exons and introns. Based on the type of domain(s), we classified the CCT family genes into CCT motif family (CMF) type, CONSTANS like (COL) type, Pseudo-response Regulator (PRR) type, and GATA and tifi containing CCT (GTCC) type. The CCT family genes of C. cajan exhibited an extensive orthologous relationship with the CCT family genes of other legume species. We also observed significant sharing of CCT family genes among the legume species. Glycine max exhibited the maximum sharing of CCT family genes with C. cajan. The analysis of CCT family proteins-based phylogenic relationships revealed a general congruence with the legumes' taxonomic relationships. The expression analysis of CCT family genes of pigeonpea demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS (CO) in ICP20338. In contrast, only CcCCT23 is active in MAL3, explaining the differential response of ICP20338 and MAL3 to photoperiod. The chromosomes of C. cajan contain a variable number of CCT family genes. A majority of these genes are localized in the centromeric regions. The COL type CCT genes are structurally highly diverse and contain a variable number of B-box domains. The CCT family genes of different legume species exhibit all three kinds of relationships: one-to-one, many-to-one, and many-to-many types. The photoperiod insensitive cultivar ICP20338 contains CcCCT4 and CcCCT23, while the photoperiod sensitive cultivar MAL3 contains only CcCCT23 as active CONSTANS (CO), which may be the plausible reason for their differential photoperiod response.

scholarly journals The Genomic Dynamics and Evolutionary Mechanism of the Pi2/9 Locus in Rice

2007 ◽  
Vol 20 (1) ◽  
pp. 63-71 ◽  
Author(s):  
Bo Zhou ◽  
Maureen Dolan ◽  
Hajime Sakai ◽  
Guo-Liang Wang
Keyword(s):  
Magnaporthe Grisea ◽  
Sequence Divergence ◽  
Valuable Insight ◽  
Gene Complex ◽  
Rice Cultivars ◽  
Orthologous Relationship ◽  
Regulatory Regions ◽  
Evolutionary Mechanism ◽  
Genetic Events ◽  
Insight Into

The Pi2/9 locus contains at least four resistance specificities to Magnaporthe grisea and belongs to a gene complex comprised of multiple genes that encode highly homologous nucleotide binding site (NBS) and leucine rich repeat (LRR) proteins. To investigate the genetic events involved in the evolution of the Pi2/9 locus, we analyzed the Pi2/9 locus at the inter- and intralocus levels in five rice cultivars. The NBS-LRR genes in the five cultivars belong to the same phylogenetic clade among rice NBS-LRR genes, and all have a phase-2 intron at the N-terminus. However, the paralogs within each haplotype show a significant sequence divergence and their N-terminal intron and 5′ regulatory regions are very different. On the contrary, the orthologs from different haplotypes are highly similar, indicating an obvious orthologous relationship has been maintained during the evolution of the Pi2/9 locus. These results suggest that sequence diversification in the 5′ regulatory regions and N-terminal introns of the paralogs may have led to suppression of meiotic recombination between the paralogs within each haplotype, facilitating the maintenance of the orthologous relationship among rice cultivars. Our observations provide valuable insight into the genomic dynamics and evolutionary mechanism of an NBS-LRR resistance-gene complex in rice.

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