Phylogenetic Analysis of KNOX Proteins

Whole genome information for Arabidopsis and rice were downloaded from the Arabidopsis Information Resource, version 10 (TAIR 10) (http://www.arabidopsis.org) and the RGAP 7 database (http://rice.plantbiology.msu.edu/), respectively. The KNOX protein sequences from Arabidopsis, rice, and Moso bamboo were aligned using ClustalX. Subsequently, to gain insights into the phylogenetic relationships among these sequences, MEGA 7.0 was used to construct the phylogenetic tree using the neighbor-joining (NJ) method [56 (link)], with 1000 bootstrap replicates. Motifs of the KNOX proteins were then analyzed using MEME [57 (link)]. Furthermore, conserved domains of the KNOX proteins were predicted by the NCBI Batch Web CDD-Search Tool (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi). Finally, the protein structures were visualized using TBtools [58 (link)].

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Jiao Y., Tan J., Guo H., Huang B., Ying Y., Ramakrishnan M, & Zhang Z. (2024). Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth. BMC Plant Biology, 24, 213.

Publication 2024

Corresponding Organization :

Other organizations : Zhejiang A & F University, Nanjing Forestry University

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Variable analysis

independent variables

Whole genome information for Arabidopsis and rice

dependent variables

Phylogenetic relationships among KNOX protein sequences from Arabidopsis, rice, and Moso bamboo
Motifs of the KNOX proteins
Conserved domains of the KNOX proteins
Protein structures of the KNOX proteins

control variables

TAIR 10 (Arabidopsis Information Resource, version 10) database
RGAP 7 (Rice Genome Annotation Project) database
ClustalX for protein sequence alignment
MEGA 7.0 for phylogenetic tree construction using the neighbor-joining (NJ) method with 1000 bootstrap replicates
MEME for motif analysis
NCBI Batch Web CDD-Search Tool for conserved domain prediction
TBtools for protein structure visualization

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