Shah, Abhijeet; Hoffman, Joseph ; Schielzeth, Holger: Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size. In: BMC genomics. Jg.20 H. 1. 2019
Inhalt
- Results
- Transcriptome assembly assessment and completeness metrics
- Transcriptome annotation and GO classification
- SNP calling and estimation of minor all frequencies (MAF)
- Scanning for expressed mitochondrial genes in assembled transcripts
- Detection of Wolbachia Pel wPip strain sequences
- Discussion
- Conclusions
- Methods
- Sample collection
- RNA extraction, cDNA library preparation and spike-in normalisation (step 1)
- Pre-processing and sequence quality control and k-mer filtering (step 2)
- Transcriptome assemblies (step 3)
- Multi-assembly merging and duplicate contig reduction (step 4)
- Transcript mapping and quantification (step 5)
- Assessment of assembled transcriptome and contig filtering (step 6 and 7)
- Annotation and sequence analysis (step 8)
- SNP calling and estimation of minor allele frequencies
- Searches for candidate green-brown pigmentation genes
- Analysis of the mitochondrial genome
- Additional files
- Abbreviations
- Acknowledgements
- Funding
- Availability of data and materials
- Authors’ contributions
- Ethics approval and consent to participate
- Consent for publication
- Competing interests
- Publisher’s Note
- References