Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Bioinformatics analysis of the light-harvesting complex (LHC) family

LY Lingyun Yuan
YZ Yushan Zheng
LN Libing Nie
LZ Liting Zhang
YW Ying Wu
SZ Shidong Zhu
JH Jinfeng Hou
GS Guo Lei Shan
TL Tong Kun Liu
GC Guohu Chen
XT Xiaoyan Tang
CW Chenggang Wang
request Request a Protocol
ask Ask a question
Favorite

To obtain the BrLhc family genes in wucai, the 34 known LHC genes published in Arabidopsis thaliana were downloaded from the TAIR genome database (https://www.arabidopsis.org/) and used as queries in a BLASTP search. The online website MEME (http://meme-suite.org/tools/meme) was used to predict the conserved motifs of the BrLhc protein sequence and construct a schematic diagram of the conserved motifs of the protein [90]. The structure of genes was visualized according to genome annotation files with TBtools [91]. MEGA7.0 software was used to compare the 47 BrLhc protein sequences of wucai, and the neighbor-joining method was used to construct a phylogenetic tree to analyze the evolutionary relationships between the BrLhcs of wucai [92]. The 2000 bp region upstream of the BrLhc genes was used as the promoter sequence by TBtools, and these sequences were submitted to Plant CARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) to predict the BrLhc promoter region cis-acting elements [93]. TBtools was used to visualize the promoter position.

Copyright and License information: The Author(s) ©2021
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A