Difference between revisions of "UGTs through the genus Brassica"

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(CoGe BLAST)
(Building a Phylogeny of Genes in the UGTs in Arabidopsis thaliana)
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==Methods==
 
==Methods==
  
===Building a Phylogeny of Genes in the UGTs in ''Arabidopsis thaliana''===
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==Building a Phylogeny of Genes in the UGTs in ''Arabidopsis thaliana''==
  
 
===CoGe BLAST===
 
===CoGe BLAST===

Revision as of 14:11, 1 April 2016

Introduction

The genus Brassica

The genus Brassica consists of over thirty wild species and hybrids or morphotypes. Generally, species from the genus Brassica are used in food like broccoli, cauliflower, cabbage and more.

The Brassica genome has undergone more polyploidy than Arabidopsis thaliana. Arabidopsis thaliana is notable for being a model organism because of its complexity paired with a relatively small genome.

Duplication Events

The Brassica genome has undergone two tetraploidy and two hexaploidy events, one more than Arabidopsis, since the eudicot paleohexaploidy event which gave rise to Vitis, Prunus, Arabidopsis, and Brassica.

Triangle of U

The "Triangle of U" theory describes the genetic relationship between six species of Brassica: Brassica rapa, Brassica nigra, Brassica oleracea, Brassica juncea, Brassica carinata, and Brassica napus. B. juncea, B. carinata and B. napus are allotetraploids, hybrids with four times the chromosome set of haploids. (Definitely want a depiction of the Triangle of U here)

UGT Gene Family

UGT functions

Uridine diphosphate (UDP) glycosyltransferases (UGTs) mediate transfer of glycosyl residues from activated nucleotide sugars to acceptor molecules (Tang, Unleashing the Genome of the Brassica rapa). They provide instructions for making enzymes that perform the process of glucuronidation, the addition of glucuronic acid to a substrate (Genetics Home Reference, UGT gene family).

UGT chemistry

By mediating transfer of glycosyl residues from activated nucleotide sugars to acceptor molecules, UGTs regulate properties of those acceptors such as bioactivity, solubility and transport within cells and throughout organisms (Ross, Higher plant glycosyltransferases).

Methods

Building a Phylogeny of Genes in the UGTs in Arabidopsis thaliana

CoGe BLAST

TAIR

Glycosyltransferase Family 1 on The Arabidopsis Information Resource (TAIR) contained each annotation by the The Institute for Genomic Research (TIGR) for flavonols and anthocyanidins which contribute to plant pigmentation. CoGe BLAST was used to find sequences corresponding to those in TAIR. After a little coding, we were able to identify from a list of over a hundred which were from the TAIR database and which were from CoGe with ease. Information including genomic locus, TIGR Annotation and Accession are in appropriately named csv files.

Finding related UGT genes in Arabidopsis lyrata

Finding related UGT genes in Brassica rapa