Identification of SAP Genes in Jatropha

To identify SAP genes in Jatropha, Pfam server (http://pfam.xfam.org/) (accessed on 31 August 2022) was searched for the A20 domain (PF01754) and AN1 domain (PF01428), and then the HMMER (https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch) (accessed on 31 August 2022) Hidden Markov model was used as a probe to screen all the candidate proteins. To ensure the reliability of the sequences and to remove redundant sequences, the search results of all candidate SAP protein sequences were further searched for the presence of A20/AN1 domains using the Pfam database (http://pfam.janelia.org/) (accessed on 31 August 2022), MOTIF search (https://www.genome.jp/tools/motif/) (accessed on 31 August 2022), NCBI conserved domain database (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) (accessed on 31 August 2022), SMART database (http://smart.embl-heidelberg.de/) (accessed on 31 August 2022), and Inter ProScan program (http://www.ebi.ac.uk/Tools/pfa/ iprscan5/) (accessed on 31 August 2022). The protein sequences of the SAP gene family of rice and Arabidopsis (Supplementary Table S1) were retrieved from the previously published report [5 (link)]. Multiple sequence alignments of all the sequences of Jatropha, Arabidopsis, and rice were performed using Muscle. Subsequently, to create a phylogenetic tree, the alignments were imported to MEGA7 software (https://www.megasoftware.net/home) (accessed on 1 September 2022) using the neighbor-joining (NJ) method with a bootstrap option of 1000 replications. The phylogenetic tree was further visualized and edited via MEGA7 software (https://www.megasoftware.net/home) (accessed on 1 September 2022) [22 (link),23 (link),24 (link),25 (link),26 (link)].

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Jalal A., Ali Q., Manghwar H, & Zhu D. (2022). Identification, Phylogeny, Divergence, Structure, and Expression Analysis of A20/AN1 Zinc Finger Domain Containing Stress-Associated Proteins (SAPs) Genes in Jatropha curcas L.. Genes, 13(10), 1766.

Publication 2022

Arabidopsis Gene Genome Jatropha Muscle Protein gene Protein sequences Proteins Replications Rice Sequence alignments

Corresponding Organization : Jiangsu University

Other organizations : Nanjing Agricultural University, Lushan Botanical Garden

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Variable analysis

independent variables

Searching the Pfam server for the A20 domain (PF01754) and AN1 domain (PF01428)
Using the HMMER Hidden Markov model to screen all the candidate proteins

dependent variables

Identifying SAP genes in Jatropha

control variables

Searching the Pfam, MOTIF, NCBI conserved domain, SMART, and InterProScan databases to ensure the reliability of the sequences and remove redundant sequences
Retrieving the protein sequences of the SAP gene family of rice and Arabidopsis from a previously published report
Performing multiple sequence alignments of all the sequences of Jatropha, Arabidopsis, and rice using Muscle
Creating a phylogenetic tree using the neighbor-joining (NJ) method with a bootstrap option of 1000 replications in MEGA7 software

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