scholarly journals Candidate genes for shell colour polymorphism in Cepaea nemoralis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3715 ◽  
Author(s):  
Jesse Kerkvliet ◽  
Tjalf de Boer ◽  
Menno Schilthuizen ◽  
Ken Kraaijeveld
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Colour Polymorphism ◽  
Snp Analysis ◽  
Nacreous Layer ◽  
Ground Colour ◽  
Cepaea Nemoralis ◽  
Excellent Starting Point

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell’s nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.

scholarly journals Candidate genes for shell colour polymorphism in Cepaea nemoralis

2017 ◽  
Author(s):  
Jesse Kerkvliet ◽  
Tjalf de Boer ◽  
Menno Schilthuizen ◽  
Ken Kraaijeveld
Keyword(s):  
Candidate Genes ◽  
Differential Expression Analysis ◽  
The Body ◽  
Colour Polymorphism ◽  
Sequence Variant ◽  
Nacreous Layer ◽  
Ground Colour ◽  
Cepaea Nemoralis ◽  
Excellent Starting Point ◽  
Starting Point

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Combining these results yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are involved in production of the shell’s nacreous layer. Comparison with morph-associated RAD-tags from a published study yielded seven transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.

scholarly journals Candidate genes for shell colour polymorphism in Cepaea nemoralis

2017 ◽  
Author(s):  
Jesse Kerkvliet ◽  
Tjalf de Boer ◽  
Menno Schilthuizen ◽  
Ken Kraaijeveld
Keyword(s):  
Candidate Genes ◽  
Differential Expression Analysis ◽  
The Body ◽  
Colour Polymorphism ◽  
Sequence Variant ◽  
Nacreous Layer ◽  
Ground Colour ◽  
Cepaea Nemoralis ◽  
Excellent Starting Point ◽  
Starting Point

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Combining these results yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are involved in production of the shell’s nacreous layer. Comparison with morph-associated RAD-tags from a published study yielded seven transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.

Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis

2014 ◽  
Vol 85 (3) ◽  
pp. 247-257 ◽  
Author(s):  
Motoki Shimizu ◽  
Ryo Fujimoto ◽  
Hua Ying ◽  
Zi-jing Pu ◽  
Yusuke Ebe ◽  
...  
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Expression Analysis ◽  
Chinese Cabbage ◽  
Differential Expression Analysis

scholarly journals Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiayi Liu ◽  
Zhou Wu ◽  
Junying Li ◽  
Haigang Bao ◽  
Changxin Wu
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Serine Phosphorylation ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Sequencing Analysis ◽  
Genome Wide

The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.

scholarly journals Best practices on the differential expression analysis of multi-species RNA-seq

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  
Keyword(s):  
Best Practices ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Single Species ◽  
Rna Seq ◽  
Species Analysis ◽  
Differential Gene ◽  
Multiple Species ◽  
Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

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