A guide to phylotranscriptomic analysis for phycologists

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Abstract: 

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.

Author(s): 
Seongmin Cheon
Sung-Gwon Lee
Hyun-Hee Hong
Hyun-Gwan Lee
Kwang Young Kim
Chungoo Park
Keywords: 
dinoflagellate
phylotranscriptomics
protocol
Link / Ref: 
Sciencegate
Attachment: 
PDF icon Phytotranscriptomic analysis for phycologists.pdf
Article Source: 
Algae 2021, 36(4): 333-340
Category: 
Basic Biology
Processing methods