植物中microRNA靶向结合的富含亮氨酸重复序列基因的计算识别

Zhu-Qing Shao; Yan-Mei Zhang; Bin Wang; Jian-Qun Chen

doi:10.21769/BioProtoc.1637

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Computational Identification of MicroRNA-targeted Nucleotide-binding Site-leucine-rich Repeat Genes in Plants

植物中microRNA靶向结合的富含亮氨酸重复序列基因的计算识别

Zhu-Qing Shao ^*

Yan-Mei Zhang ^*

Bin Wang

Jian-Qun Chen email

(*contributed equally to this work) 发布: 2015年11月05日第5卷第21期 DOI: 10.21769/BioProtoc.1637 浏览次数: 10413

评审: Tie LiuAlberto Carbonell

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参见作者原研究论文

The authors used this protocol in:

Cover of Plant Physiology, featuring study using the protocol.

Sep 2014

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Abstract

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen infection. Recent studies have revealed that microRNAs are involved in regulation of NBS genes in plants (Zhai et al., 2011; Shivaprasad et al., 2012). This protocol describes computational methods for the genome-wide identification of plant NBS genes potentially regulated by microRNAs.

Equipment

Personal computer (an internet connection is needed) (Intel Core i5-2300 CPU, 8 GB RAM)

Sequence data and software

Sequence data compilation
The coding sequence (CDS) and protein sequences of interested genomes should be downloaded from relevant databases. A recommended database containing a relatively large number of sequenced plant genomes is Phytozome (http://www.phytozome.org/) (Goodstein et al., 2012). MicroRNAs of interested genomes can be retrieved from the miRBase (http://www.mirbase.org/) (Kozomara and Griffiths-Jones, 2014) or from in-house sequenced data.
Required software and online tools
The following software should be locally installed in your computer:
1. Hmmer 3.0 (http://hmmer.janelia.org/) (Johnson et al., 2010), for perform local hidden Markov models (HMM) search of NBS homologous proteins.
2. NCBI BLAST⁺ or NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi), for perform local blastp search of NBS homologous proteins.
3. ActivePerl 5.14.2 (http://www.activestate.com/activeperl/downloads), for running scripts written in perl language.
Manuals for installation/operation of these softwares could be downloaded in the referred websites.
1. The online tools to be used are:
2. COILS (http://www.ch.embnet.org/software/COILS_form.html) (Lupas et al., 1991), a program for identification of coiled-coils (CC) domain in protein sequences.
3. Pfam (http://pfam. sanger.ac.uk/) (Finn et al., 2014), a database for identification of protein domains.
4. psRNATarget (http://plantgrn.noble.org/psRNATarget/) (Dai and Zhao, 2011), a website designed for prediction microRNA targets in plants.

Procedure

English

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文章信息

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如何引用

Readers should cite both the Bio-protocol article and the original research article where this protocol was used:

Shao, Z., Zhang, Y., Wang, B. and Chen, J. (2015). Computational Identification of MicroRNA-targeted Nucleotide-binding Site-leucine-rich Repeat Genes in Plants. Bio-protocol 5(21): e1637. DOI: 10.21769/BioProtoc.1637.
Shao, Z. Q., Zhang, Y. M., Hang, Y. Y., Xue, J. Y., Zhou, G. C., Wu, P., Wu, X. Y., Wu, X. Z., Wang, Q., Wang, B. and Chen, J. Q. (2014). Long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family. Plant Physiol 166(1): 217-234.