title: Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data.
abstract: The life cycle of Plasmodium falciparum is very complex, with an erythrocytic stage that involves the invasion of red blood cells and the survival and growth of the parasite within the host. Over the past several decades, numbers of studies have shown that proteins exported by P. falciparum to the surface of infected red blood cells play a critical role in recognition and interaction with host receptors and are thus essential for the completion of the life cycle of P. falciparum. However, little is known about long noncoding RNAs (lncRNAs). In this study, we designed a computational pipeline to identify new lncRNAs of P. falciparum from published RNA-seq data and analyzed their sequences and expression features. As a result, 164 novel lncRNAs were found. The sequences and expression features of P. falciparum lncRNAs were similar to those of humans and mice: there was a lack of sequence conservation, low expression levels, and high expression coefficient of variance and co-expression with nearby coding sequences in the genome. Next, a coding/noncoding gene co-expression network for P. falciparum was constructed to further annotate the functions of novel and known lncRNAs. In total, the functions of 69 lncRNAs, including 44 novel lncRNAs, were annotated. The main functions of the lncRNAs included metabolic processes, biosynthetic processes, regulation of biological processes, establishment of localization, catabolic processes, cellular component organization, and interspecies interactions between organisms. Our results will provide clues to further the investigation of interactions between human hosts and parasites and the mechanisms of P. falciparum infection.
authors: Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, People's Republic of China.
authors: Qi
authors: Q
authors: Liao
authors: Jia
authors: J
authors: Shen
authors: Jianfa
authors: J
authors: Liu
authors: Xi
authors: X
authors: Sun
authors: Guoguang
authors: G
authors: Zhao
authors: Yanzi
authors: Y
authors: Chang
authors: Leiting
authors: L
authors: Xu
authors: Xuerong
authors: X
authors: Li
authors: Ya
authors: Y
authors: Zhao
authors: Huanqin
authors: H
authors: Zheng
authors: Yi
authors: Y
authors: Zhao
authors: Zhongdao
authors: Z
authors: Wu
mesh_terms: D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling; D018503:Genome, Protozoan; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010963:Plasmodium falciparum / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D016053:RNA, Protozoan / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding; D016053:RNA, Protozoan