De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters

Abstract

Hamsters are an ideal animal model for a variety of biomedical research areas such as cancer, virology, circadian rhythms, and behavioural neuroscience. The use of hamsters has declined, however, most likely due to the dearth of genetic tools available for these animals. Our laboratory uses hamsters to study acute social stress, and we are beginning to investigate the genetic mechanisms subserving defeat-induced behavioural change. We have been limited, however, by the lack of genetic resources available for hamsters. In this study, we sequenced the brain transcriptome of male and female Syrian hamsters to generate the necessary resources to continue our research. We completed a de novo assembly and after assembly optimization, there were 113,329 transcripts representing 14,530 unique genes. This study is the first to characterize transcript expression in both female and male hamster brains and offers invaluable information to promote understanding of a host of important biomedical research questions for which hamsters are an excellent model.

Inferior Colliculus Transcriptome After Status Epilepticus in the Genetically Audiogenic Seizure-Prone Hamster GASH/Sal

“…In this study, Actb was used as the reference gene because it was the most stable gene according to the expression level measured by NormFinder software in the intra-and intergroup analyses (Andersen et al, 2004),. Moreover, it has been previously reported that the Gapdh gene is overexpressed in the Syrian hamster (McCann et al, 2017). Reference genes make it possible to normalize the amount of cDNA used in each reaction.…”

Dominance relationships in Syrian hamsters modulate neuroendocrine and behavioral responses to social stress

“…The expression of tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) or glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA served as an internal control. As gene specific primers for Syrian hamsters were not available at the time of this study (but see McCann, Sinkiewicz, Norvelle, & Huhman, 2017), we used the National Center for Biotechnology Information (NCBI) GenBank databases to perform BLAST analyses with known mouse gene sequences and predicted Syrian hamster sequences (NCBI Syrian hamster reference sequences: CRH: XM_005066742.2; YWHAZ: XM_021228739.1; GAPDH: XM_013124485.1). BLAST analyses revealed a significant overlap in mouse and hamster gene sequences (CRH: 88%; YWHAZ: 94%; GAPDH: 92%), therefore mouse gene specific primers were used (Bio-Rad, Hercules, CA; Table 1).…”

Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

“…were quite low (Table S1) which is understood because Carrizo citrange is a hybrid. Assembly optimization was done to keep only biologically meaningful transcripts and to save statistical power in the differential expression analysis (McCann et al, 2017;Ono et al, 2015). Initial differential expression was done by using both coding isoforms counts and unigene counts.…”

“…After reference genome mapping, reads mapped to P.parasitca genomes were filtered out and pathogen free clean reads from all seven samples were used to generate a pooled de novo transcriptome assembly using Trinity (Grabherr et al, 2011), one of the most widely used de novo transcriptome assembler for short reads in both animal (Hsu et al, 2017;McCann et al, 2017) and plant transcriptome studies (Evangelisti et al, 2017;Guo et al, 2016;Xiong et al, 2017;Yang et al, 2017). Altogether, 60874 trinity genes and 87299 trinity assembled transcripts were obtained with an N50 values of 1428 bp and 1796 bp, respectively (Table 1).…”

“…Trinity transcripts are artificially assembled so chances of redundant transcripts are high. Thus, before moving further an optimization of Trinity constructed de novo assembly is necessary to get rid of false positives and to save statistical power in the downstream analysis (McCann et al, 2017;Ono et al, 2015). Assembly optimization was done by running homology-based search using BLAST and Pfam on Transdecoder predicted ORFs (see methods for detail) and 21,278 coding unigenes comprised of 40,943 coding transcripts were obtained (Table 1).…”