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In Silico Identification and Characterization of Starch Synthase (ss) Genes in Potato (solanum Tuberosum)

Atiqur Rahman
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Jobadatun Naher
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Zahid Hasan Sabuj
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Ujjal Kumar Nath
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Abstract/ Executive Summary:

Starch is the major source of storage carbohydrates, which is an important product for plants and animals as well as for industrial use. Starch synthase (SS) enzyme encoded by several genes is the key factor in the starch biosynthetic pathway. Genome wide exploration and characterization of these starch synthase (SS) genes are still limited in the literature. Therefore, intensive bioinformatic tools were approached to identify and in silico characterize the SS genes in potato genome. We identified several orthologues of SS in Arabidopsis by using the term starch synthase in Arabidopsis genome database (TAIR) and National Centre for Biotechnology Information (NCBI). These orthologues were blasted in Sol Genomics network and ten SS genes were confirmed as members of the family following Hidden Markov Model (HMM). The genes were characterized in silico for chromosomal locations, phylogeny, exonintron, domains and motif content, molecular weight and nature of proteins and predicted the functions using different online bioinformatic tools. Chromosomal maps and phylogenetic trees were constructed for analyzing evolutionary patterns and relationships with the SS genes of other crop species. The SS genes are distributed on 4 chromosomes (chromosome number 2, 3, 7 and 8) out of 12 potato basic chromosomes and originated from Arabidopsis. The results of this study will be provided basic information in planning future research regarding the regulatory mechanism of search synthesis both under normal and stress conditions.

Keywords: In silico, Starch synthase, Potato, Phylogeny, Motif

Location: Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Start Date:

End Date:

Program Area: Crop-Soil-Water Management

Commodity: Potato

Objectives:

To computationally characterize the structure, chromosomal locations, function and evolutionary divergence and to classify them based on phylogenetic analysis.

Methodology:

Identification of starch synthase gene: For genome wide identification of potato starch synthase (SS) genes, the keyword starch synthase was used as a query to find out orthologue in Arabidopsis using Arabidopsis genome database (TAIR) and National Centre for Biotechnology Information (NCBI). The redundant sequences were discarded from blast search in Sol Genomic network (http://solgenomics.net/) and NCBI (https://www.ncbi.nlm.nih.gov/) and finally, 10 genes were identified and confirmed through Hidden Markov Model (HMM) ENSEMBLE PLANT (http://plants.ensembl.org/hmmer/index.html). Arabidopsis starch synthase domain sequences were used to compare with predicted potato starch synthase domain sequences for the confirmation using the web tool from EMBL (http://smart.embl-heidelberg.de/). CDS (coding sequence) and protein sequences of the potato SS genes were obtained from SGN (https://solgenomics.net/). To verify further the identified sequences were checked in NCBI (https://www.ncbi.nlm.nih.gov/) and iTAK; Plant Transcription factor & Protein Kinase Identifier and Classifier (http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi). Sequence analysis of potato starch synthase genes: ProtParam (http://web.expasy.org/protparam/) was used to analyze the primary structure, comprising the molecular weight (MW), the length and isoelectric point (pI) of the assumed potato starch synthase proteins. The exon/intron structures of the potato SS genes were analyzed by GSDS (http://gsds.cbi.pku.edu.cn/) web tool using the potato SS genes CDS and their corresponding genomic sequences. To analyze the potato starch synthase protein motifs, software MEME (http://memesuite.org/) was used. The following parameters were used to identify distinctive motifs; (1) a maximum number of motifs 10, (2) width of the optimum motif ≥ 6. Clustal omega web tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi) was used to analyze the similarity among the 10 potato starch synthase proteins. ProtComp 9.0 from SoftBerry (http://linux1.softberry.com/berry.phtml) was used to predict the subcellular locations of the SS proteins of potato. Phylogenetic analysis of potato starch synthase (SS) proteins. The deduced amino acid sequences of Arabidopsis, tomato, tobacco and rice SS proteins were obtained from TAIR, SGN, NCBI, respectively and aligned with the help of DNAMAN web server. These aligned sequences were used to construct a phylogenetic tree using UPAGMA method with 1000 bootstrap replicates in MEGA-X software. A second phylogenetic tree of the full-length amino acid sequences of 10 potato SS proteins was constructed using the maximum parsimony method following the complete deletion of amino acids with 1000 bootstrap replicates. Chromosomal locations, gene duplication analysis of potato SS genes: The start and end positions of each potato SS gene, including sub-genome information, were obtained from SGN and the position of each genes was analyzed using the MapGene2Chromosome2 (http://mg2c.iask.in/) web tool. An NCBI BLAST search was conducted based on the query coverage percentage of the potato SS genes against each other to identify duplicated genes and to identify each gene. When the query coverage percentage and identity of the candidate genes were ≥80%, they were considered to be segmentally duplicated genes. Paralogous genes were considered to be tandemly duplicated when two genes were separated by five or fewer genes in a 100-kb region on a chromosome.

Source of Information: J Bangladesh Agril Univ 18(S1): 816–823, 2020 ISSN 1810-3030 (Print) 2408-8684 (Online)

Article Link (Online Journal): https://doi.org/10.5455/JBAU.13032

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

Starch synthase (SS) gene family has been characterized in several plants. In this study, we identified 10 SS genes in Solanum tuberosum and categorize them with other crops. These results showed the relationship among them. The results of this study provide foundation for further investigation of biological function of this gene family in potato as well as in other crops under both normal and stress conditions.

Knowledge Management: Journal