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Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data

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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.

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Acknowledgments

This work was supported by the National Basic Research Program of China (2010CB530004), National Natural Science Foundation of China (31301084), Natural Science Foundation of Zhejiang Province of China (LQ13C060002), and the K.C. Wong Magna Fund of Ningbo University.

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Authors and Affiliations

  1. Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, People’s Republic of China

    Qi Liao, Jianfa Liu & Leiting Xu

  2. Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China

    Jia Shen, Xi Sun, Xuerong Li, Huanqin Zheng & Zhongdao Wu

  3. Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, People’s Republic of China

    Guoguang Zhao & Yi Zhao

  4. The Pathogen Biology Laboratory, The Fourth Military Medical University, Xian, People’s Republic of China

    Ya Zhao

  5. Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, People’s Republic of China

    Yanzi Chang

  6. Key Laboratory for Tropical Diseases Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, People’s Republic of China

    Jia Shen, Xi Sun, Xuerong Li & Huanqin Zheng

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  1. Qi Liao
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  2. Jia Shen
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  4. Xi Sun
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  7. Leiting Xu
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  9. Ya Zhao
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  10. Huanqin Zheng
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  11. Yi Zhao
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  12. Zhongdao Wu
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Corresponding authors

Correspondence to Yi Zhao or Zhongdao Wu.

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Qi Liao and Jia Shen contributed equally to this study.

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ESM Table 1

Gtf file of 164 novel lncRNA candidates of P. falciparum. (TXT 25 kb)

ESM Table 2

Co-located pairs of novel lncRNAs and protein-coding genes for which the distance between their genomic regions is less than 1 kb. (XLS 22 kb)

ESM Table 3

Specific protein coding genes and lncRNAs. (XLS 18 kb)

ESM Table 4

Predicted functions of lncRNAs by the hub-based method. (XLS 344 kb)

ESM Table 5

Predicted functions of lncRNAs by the module-based method. (XLS 247 kb)

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Liao, Q., Shen, J., Liu, J. et al. Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data. Parasitol Res 113, 1269–1281 (2014). https://doi.org/10.1007/s00436-014-3765-4

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