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The Korean Society of Phycology (한국조류학회(藻類))
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A guide to phylotranscriptomic analysis for phycologists

  • Cheon, Seongmin (School of Biological Science and Technology, Chonnam National University) ;
  • Lee, Sung-Gwon (School of Biological Science and Technology, Chonnam National University) ;
  • Hong, Hyun-Hee (School of Biological Science and Technology, Chonnam National University) ;
  • Lee, Hyun-Gwan (Department of Oceanography, Chonnam National University) ;
  • Kim, Kwang Young (Department of Oceanography, Chonnam National University) ;
  • Park, Chungoo (School of Biological Science and Technology, Chonnam National University)
  • Received : 2021.10.11
  • Accepted : 2021.12.07
  • Published : 2021.12.15
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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.

Keywords

Acknowledgement

We thank the CSB lab members. This research was supported by the Basic Science Research Program of the National Research Foundation of Korea (NRF), funded by the Ministry of Education (NRF-2019R1F1A1062411 to CP, NRF-2016R1A6A1A03012647 to H-G Lee, NRF-2020R1A2C3005053 to KYK) and by the "Research center for fishery resource management based on the information and communication technology," funded by the Ministry of Oceans and Fisheries, Korea (2021, grant number 20180384 to CP).

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