title: Computational prediction of microRNAs and their targets from three unicellular algae species with complete genome sequences.
abstract: The genome sequences of Phaeodactylum tricornutum, Thalassiosira pseudonana, and Cyanidioschyzon merolae have provided significant evidence for the secondary endosymbiosis of diatoms in regard to the genome. Yet little about their relationships in regard to gene regulation pattern, such as microRNA (miRNA), has been reported. Using a homology search based on genomic sequences, 13, 3, and 7 predicted miRNA genes were found in genomes from P. tricornutum, T. pseudonana, and C. merolae, respectively. Of the 23 miRNA genes, 18 had homology with animal miRNAs, implying that they are ancestral miRNAs. A phylogenetic tree based on common miRNA families shared by these three unicellular algae, higher plants, and animals showed that P. tricornutum shared most miRNAs with animals. The phylogenetic tree also showed that C. merolae shared more miRNAs with plants than did the two diatoms, and the majority of its miRNAs were shared with the two diatoms. Our results were consistent with diatoms originating from a secondary endosymbiosis.
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao 266071, People's Republic of China.
authors.forename: Aiyou
authors.initials: A
authors.lastname: Huang
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Wu
authors.forename: Guangce
authors.initials: G
authors.lastname: Wang
authors.forename: Zhaojun
authors.initials: Z
authors.lastname: Jia
authors.forename: Linwen
authors.initials: L
authors.lastname: He
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017377:Diatoms / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D016678:Genome; D035683:MicroRNAs / Q000235:genetics*; D010802:Phylogeny; D018749:RNA, Plant / Q000235:genetics; D000461:Rhodophyta / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant