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Chemogenomic Profiling of the Fungal Pathogen Candida albicans.

Author(s): Chen Y, Mallick J, Maqnas A, Sun Y, Choudhury BI, Côte P, Yan L, Ni TJ, Li Y, Zhang D, Rodríguez-Ortiz R, Lv QZ, Jiang YY, Whiteway M

Antimicrob Agents Chemother. 2018 02;62(2): Authors: Chen Y, Mallick J, Maqnas A, Sun Y, Choudhury BI, Côte P, Yan L, Ni TJ, Li Y, Zhang D, Rodríguez-Ortiz R, Lv QZ, Jiang YY, Whiteway M

Article GUID: 29203491
Evolutionary Transition of GAL Regulatory Circuit from Generalist to Specialist Function in Ascomycetes.

Author(s): Choudhury BI, Whiteway M

Trends Microbiol. 2018 08;26(8):692-702 Authors: Choudhury BI, Whiteway M

Article GUID: 29395731
Erratum for Chen et al., "Chemogenomic Profiling of the Fungal Pathogen Candida albicans".

Author(s): Chen Y, Mallick J, Maqnas A, Sun Y, Choudhury BI, Côte P, Yan L, Ni TJ, Li Y, Zhang D, Rodríguez-Ortiz R, Lv QZ, Jiang YY, Whiteway M...

Antimicrob Agents Chemother. 2018 04;62(4): Authors: Chen Y, Mallick J, Maqnas A, Sun Y, Choudhury BI, Côte P, Yan L, Ni TJ, Li Y, Zhang D, Rodríguez-Ortiz R, Lv QZ, Jiang YY, Whiteway M...

Article GUID: 29588354
Functional androdioecy in critically endangered Gymnocladus assamicus (Leguminosae) in the Eastern Himalayan Region of Northeast India.

Author(s): Choudhury BI, Khan ML, Dayanandan S

PLoS One. 2014;9(2):e87287 Authors: Choudhury BI, Khan ML, Dayanandan S

Article GUID: 24586267
Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India.

Author(s): Choudhury BI, Khan ML, Dayanandan S

BMC Genet. 2014 Jun 16;15:71 Authors: Choudhury BI, Khan ML, Dayanandan S

Article GUID: 24935343
Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.

Author(s): Choudhury BI, Khan ML, Dayanandan S

BMC Res Notes. 2014 Dec 29;7:953 Authors: Choudhury BI, Khan ML, Dayanandan S

Article GUID: 25547027
Rewiring of the Ppr1 Zinc Cluster Transcription Factor from Purine Catabolism to Pyrimidine Biogenesis in the Saccharomycetaceae.

Author(s): Tebung WA, Choudhury BI, Tebbji F, Morschhäuser J, Whiteway M

Curr Biol. 2016 07 11;26(13):1677-1687 Authors: Tebung WA, Choudhury BI, Tebbji F, Morschhäuser J, Whiteway M

Article GUID: 27321996
Title:Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India.
Authors:Choudhury BI,  Khan ML,  Dayanandan S
Link:https://www.ncbi.nlm.nih.gov/pubmed/24935343?dopt=Abstract
DOI:10.1186/1471-2156-15-71
Category:BMC Genet
PMID:24935343
Dept Affiliation: BIOLOGY
1 Forest and Evolutionary Genomics Laboratory and Centre for Structural and Functional Genomics, Biology Department, Concordia University Montréal, 7141 Sherbrooke St, West, Montréal, Quebec H4B 1R6, Canada. baharul.choudhury@concordia.ca.

Description:

Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India.

BMC Genet. 2014 Jun 16;15:71

Authors: Choudhury BI, Khan ML, Dayanandan S

Abstract

BACKGROUND: During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus.

RESULTS: No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (ptot = 0.0053) than nonglutinous type varieties (ptot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (ptot = 0.0010) than in the colored apiculus varieties (ptot = 0.0023).

CONCLUSIONS: The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.

PMID: 24935343 [PubMed - indexed for MEDLINE]