Vol 52(2018) N 4 p. 520-531; DOI 10.1134/S0026893318040167
L.G. Popova1*, D.V. Belyaev1 , A.V. Shuvalov1, A.A. Yurchenko2, D.A. Matalin1, D.E. Khramov1,3, Y.V. Orlova1, Y.V. Balnokin1,3
In silico Analyses of Transcriptomes of the Marine Green Microalga Dunaliella tertiolecta: Identification of Sequences Encoding P-type ATPases1Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276 Russia
2Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199034 Russia
3Moscow State University, Department of Biology, Moscow, 119192 Russia
Received - 2017-12-14; Accepted - 2018-02-01
De novo assembled transcriptomes of the marine microalga Dunaliella tertiolecta (Chlorophyta) were analyzed. Transcriptome assemblies were performed using short-read RNA-seq data deposited in the SRA database (DNA and RNA Sequence Read Archive, NCBI). A merged transcriptome was assembled using a pooled RNA-seq data set. The goal of the study was in silico identification of nucleotide sequences encoding P-type ATPases in D. tertiolecta transcriptomes. P-type ATPases play a considerable role in the adaptation of an organism to a variable environment, and this problem is particularly significant for microalgae inhabiting an environment with an unstable ionic composition. Particular emphasis was given to searching for a sequence coding Na+-ATPase. This enzyme is expected to function in the plasma membrane of D. tertiolecta like in some marine algae, in particular, in the closely related alga Dunaliella maritima. An ensemble of 12 P-type ATPases consisting of members belonging to the five main subfamilies of the P-type ATPase family was revealed in the assembled transcriptomes. The genes of the following P-type ATPases were found: (1) heavy metal ATPases (subfamily PIB); (2) Ca2+-ATPases of SERCA type (subfamily P2A); (3) H+-ATPases (subfamily P3); (4) phospholipid-transporting ATPases (flippases) (subfamily P4); (5) cation-transporting ATPases of uncertain specificities (subfamily P5). The presence of functional Na+-ATPases in marine algae is presently undoubted. However, contrary to expectations, we failed to find a nucleotide sequence encoding a protein that could unequivocally be considered a Na+-ATPase. Further study is necessary to elucidate the roles of in silico revealed D. tertiolecta ATPases in Na+ transport.
Dunaliella tertiolecta, P-type ATPases, marine microalgae, de novo transcriptome assembly