Project
Phylogenetic analysis of SPATA31 genes.
Students: Ece Zeynep Atici and Baris Caglar
Supervisor: Cemalettin Beckpen
Aim of my research is to identify presence of SPATA31 gene family in carnivores. SPATA31 gene is an adaptive gene that is shown to be expanded in humans. Specific types that I was interested in for SPATA31 gene search in carnivores are type A and C copies, as they are the duplicated versions present in humans. Generating phylogenetic trees and performing multiple alignment analyses with available datasets were the followed approaches to determine what types and copy number are present in carnivores. In addition, transcriptional analyses were performed with Galaxy Server to observe which tissues of carnivores expressed SPATA31A genes.
Figure showing Neighbor-joining phylogenetic tree of SPATA31 protein of primates, rodents and carnivores. Obtained clusters have branched out according to known clades with the exceptions of Guinee pig (Cavia porcellus) and naked mole rat (Heterocephalus glaber) as they are placed closer to primates compared to rodents with a confidence of 45%. Panda (Ailuropoda melanoleuca) is observed to be the outlier within the cluster of carnivores. Data used for rodents and carnivores were extracted from NCBI and UCSC Genome Browser databases and primate data was provided by Assistant Prof. Cemalettin Bekpen. Protein coding long exon of human SPATA31C gene was used to obtain data used for generation of the phylogenetic tree as it is one of the highly conserved member of SPATA31 gene family. NCBI Blast, BLAT, SMART and ExPASy translate were utilized. Multiple sequence alignment and CNV analyses were performed multiple times at different dates to confirm our results and use the most up-to-date data.