Glycine Max Sequence Alignment and Phylogenetic Tree Analysis Report

This report provides a bioinformatics analysis of Glycine max, focusing on sequence alignment and phylogenetic tree construction. The report examines the process of aligning DNA, protein, or RNA sequences to identify regions of similarity between species, using tools like MSA (Clustal W). The analysis includes a multiple sequence alignment of GmWRI1 protein and CLE protein of Glycine max, comparing it with sequences from related species found in the plant ENSEMBL database such as Arabidopsis thaliana, Medicago truncatula, Oryza sativa, and Vitis vinifera. The phylogenetic tree illustrates the evolutionary relationships between these species. Homology searches using BLAST tools and Hidden Markov Models are also discussed, revealing the mapping of SWEET genes to soybean chromosomes. Furthermore, the report highlights the expression profiles of SWEET genes across different developmental stages and tissues, indicating their association with reproductive tissue development. The analysis contributes to understanding the genetic makeup and evolutionary relationships of Glycine max.

Running head: BIOINFORMATICS
GLYCINE MAX
Name of the Student
Name of the University
Author Note

1BIOINFORMATICS
Sequence alignment
Sequence alignment is the process of arranging the DNA, protein or RNA in order to identify the
region of similarity in between two or more species. This region may be a consequence of structural,
functional or an evolutionary relationship between the sequences. The figure below shows the multiple
sequence alignment of GmWRI1 protein of Gycine max between different species. The gaps are inserted
in between the residues so that the similar characteristics are identified successfully with alignment.
According to the plant ENSEMBL database, Glycine max has four related groups named as Arabidopsis
thaliana¸ Medicago truncatula, Oryza sativa and Vitis vinifera (Beligala. et al. 2017)

2BIOINFORMATICS
Fig 1: Multiple sequence alignment of Glycine max
Source: ENSEMBL
The alignment process has been performed with the help of MSA (Clustal W). This tool
is used for multiple sequence alignment.
Phylogenetic tree
A phylogenetic tree is defined as a branching diagram which shows an evolutionary
relationship between the individuals of biological species groups and other entities. Based on
their similarity and differences, these organisms are grouped into various classes. These trees are
very useful in biological fields such as systematics, phylogenetic and bioinformatics (Ahmad et
al. 2019).

3BIOINFORMATICS
Fig 2: Glycine max (phylogenetic tree)
Source: NCBI database
The process of homology searches was performed using BLAST tools and the Hidden Markov
Model showed that the sequence alignments between 52 SWEET genes were perfectly mapped
to the fifteen soya bean chromosome. A broad range of expression profile has been shown in
different developmental stages and different tissues. The analysis of expression profiling and
public transcriptome data by using QRT-PCR shows that majority of the SWEET genes of
Glycine max were associated with reproductive tissue development. This gene family has been
studied in this paper because it holds a broad category in the family of Glycine max. This
experiment has not been conducted to date with the sweet genes of Glycine max.

4BIOINFORMATICS
References
Ahmad, M.Z., Sana, A., Jamil, A., Nasir, J.A., Ahmed, S. and Hameed, M.U., 2019. A genome-
wide approach to the comprehensive analysis of GASA gene family in Glycine max. Plant
molecular biology, 100(6), pp.607-620.
Beligala, D.H., Michaels, H.J., Devries, M. and Phuntumart, V., 2017. Multilocus sequence
analysis of root nodule bacteria associated with Lupinus spp. and Glycine max. Advances in
Microbiology, 7(11), pp.790-812.