Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication

2014 ◽  
Vol 290 (2) ◽  
pp. 521-530 ◽  
Author(s):  
Panneerselvam Krishnamurthy ◽  
Joon Ki Hong ◽  
Jin A Kim ◽  
Mi-Jeong Jeong ◽  
Yeon-Hee Lee ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Evolutionary Dynamics ◽  
Whole Genome ◽  
Genome Wide Analysis ◽  
Expansin Gene ◽  
Genome Wide ◽  
Genome Triplication

scholarly journals Genome-Wide Analysis of the Expansin Gene Superfamily Reveals Grapevine-Specific Structural and Functional Characteristics

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62206 ◽  
Author(s):  
Silvia Dal Santo ◽  
Alessandro Vannozzi ◽  
Giovanni Battista Tornielli ◽  
Marianna Fasoli ◽  
Luca Venturini ◽  
...  
Keyword(s):  
Functional Characteristics ◽  
Genome Wide Analysis ◽  
Expansin Gene ◽  
Genome Wide

scholarly journals Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1887
Author(s):  
Natalia V. Dementieva ◽  
Andrei A. Kudinov ◽  
Tatiana A. Larkina ◽  
Olga V. Mitrofanova ◽  
Artyom P. Dysin ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Germplasm Collection ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Breeding Programs ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Rare And Endangered ◽  
Chicken Breeds ◽  
Conservation Breeding

Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.

scholarly journals Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa

PLoS ONE ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. e0151522 ◽  
Author(s):  
Parameswari Paul ◽  
Vignesh Dhandapani ◽  
Jana Jeevan Rameneni ◽  
Xiaonan Li ◽  
Ganesan Sivanandhan ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Hequan Sun ◽  
Beth A. Rowan ◽  
Pádraic J. Flood ◽  
Ronny Brandt ◽  
Janina Fuss ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Whole Genome ◽  
Fine Scale ◽  
Simultaneous Generation ◽  
Genome Wide Analysis ◽  
Recombinant Plant ◽  
Genome Wide ◽  
Large Populations

Abstract Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.

scholarly journals Induction of theCandida albicansFilamentous Growth Program by Relief of Transcriptional Repression: A Genome-wide Analysis

2005 ◽  
Vol 16 (6) ◽  
pp. 2903-2912 ◽  
Author(s):  
David Kadosh ◽  
Alexander D. Johnson
Keyword(s):  
Candida Albicans ◽  
Transcriptional Repression ◽  
Fungal Pathogen ◽  
Morphological Transition ◽  
Whole Genome ◽  
Transcriptional Repressors ◽  
Genome Wide Analysis ◽  
Human Fungal Pathogen ◽  
Genome Wide ◽  
A Genome

Candida albicans, the major human fungal pathogen, undergoes a reversible morphological transition from blastospores (round budding cells) to filaments (elongated cells attached end-to-end). This transition, which is induced upon exposure of C. albicans cells to a number of host conditions, including serum and body temperature (37°C), is required for virulence. Using whole-genome DNA microarray analysis, we describe 61 genes that are significantly induced (≥2-fold) during the blastospore to filament transition that takes place in response to exposure to serum and 37°C. We next show that approximately half of these genes are transcriptionally repressed in the blastospore state by three transcriptional repressors, Rfg1, Nrg1, and Tup1. We conclude that the relief of this transcriptional repression plays a key role in bringing the C. albicans filamentous growth program into play, and we describe the framework of this transcriptional circuit.

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