Poster_Punzi3.pdf (18.45 MB)
Clams and paternal mitochondria inheritance
poster
posted on 2017-07-18, 15:18 authored by Elisabetta PunziElisabetta Punzi, Liliana MilaniLiliana Milani, Fabrizio GhiselliFabrizio Ghiselli, Marco PassamontiMarco PassamontiThe dataset:
RNA-seq libraries prepared from ripe gonads of 12 individuals (six males and six females) of R. decussatus and R.philippinarum (protocol in Mortazavi et al. 2008 with modification from Ghiselli et al. 2012) have been assembled according to Ghiselli et al. 2012.
Differential transcription is expressed as the binary logarithm of the fold change [log2(FC)]; male-biased transcripts are defined as those having a log2(FC) smaller than -1, whereas female-biased ones have a log2(FC) bigger than 1.
Annotation was performed with a pipeline specifically designed for non-model organism transcriptome annotation (Ghiselli et al, in preparation).
Mitochondrial targeting was assessed using TargetP (Emanuelsson et al. 2007).
Data analysis:
Two different methods were used to extract sequences of interest:
Autophagy and mitophagy are evolutionary conserved pathways. Therefore, lists of Homo sapiens and the oyster Crassostrea gigas orthologs implicated in these two patwhays were downloaded from KEGG and used to query R. decussatus and R. philippinarum transcriptomes with a local BLASTP.
Endonucleases, polymerases and the Ubiquitin-proteasome system, instead, are composed of proteins with diversified structures and evolutionary history. As such, sequences belonging to these pathways were extracted using their GO annotation.
RNA-seq libraries prepared from ripe gonads of 12 individuals (six males and six females) of R. decussatus and R.philippinarum (protocol in Mortazavi et al. 2008 with modification from Ghiselli et al. 2012) have been assembled according to Ghiselli et al. 2012.
Differential transcription is expressed as the binary logarithm of the fold change [log2(FC)]; male-biased transcripts are defined as those having a log2(FC) smaller than -1, whereas female-biased ones have a log2(FC) bigger than 1.
Annotation was performed with a pipeline specifically designed for non-model organism transcriptome annotation (Ghiselli et al, in preparation).
Mitochondrial targeting was assessed using TargetP (Emanuelsson et al. 2007).
Data analysis:
Two different methods were used to extract sequences of interest:
Autophagy and mitophagy are evolutionary conserved pathways. Therefore, lists of Homo sapiens and the oyster Crassostrea gigas orthologs implicated in these two patwhays were downloaded from KEGG and used to query R. decussatus and R. philippinarum transcriptomes with a local BLASTP.
Endonucleases, polymerases and the Ubiquitin-proteasome system, instead, are composed of proteins with diversified structures and evolutionary history. As such, sequences belonging to these pathways were extracted using their GO annotation.
