Phylogenetic and Molecular Evolutionary Analysis of Plants

Plant systems and evolutionary biology is an increasingly comprehensive field of study that investigates the origins of plant species diversity, the mechanisms of diversification, and their evolution. Plants have evolved through a very complex evolutionary process, during which many genes were generated along potentially divergent routes. Phylogenetic network diagrams provide a clear picture of the complex web of evolutionary relationships, including both vertical and horizontal evolution.

Lifeasible, a leading biotechnology company, has been working intensively on the evolutionary analysis of plants. Our advanced plant gene sequencing platform and diverse bioinformatics tools enable us to reveal the origin and evolutionary history of new plant traits based on comparative evolutionary genomics. We provide our clients with phylogenetic and molecular evolutionary analysis services based on a "scientific, precise, and customizable" service philosophy.

What We Offer

During the evolution of a species, there are two main types of evolutionary routes for different genes: vertical evolutionary processes and horizontal evolutionary processes. Our analysis service can summarize these two evolutionary processes in a network diagram, helping our clients to gain a clearer understanding of the molecular evolution of plants.

• Transcriptome Sequencing

The target plant samples were quickly put into liquid nitrogen and frozen, and total RNA was extracted. The cDNA was amplified using PCR and sequenced after constructing a sequencing library.

• Sequence Assembly and ORF Prediction

After high-throughput sequencing, the raw image data was converted into sequence data, i.e., raw reads, and stored in FASTQ format. The clean data was obtained by removing splice sequences and low-quality sequences at both ends, and the open reading frame (ORF) prediction was performed to obtain the best ORF region in the sequence.

• Transcriptome Data Integrity Assessment

It is essential to assess whether the transcript sequences obtained from sequencing assemblies cover all possible transcripts. This is directly related to the size and completeness of the data in the phylogenetic analysis and, thus, to the phylogenetic tree's topology.

• Direct Homologous Gene Screening

1. Genomic data and protein sequences of the target plant species were obtained by downloading from the database website.
2. The software was used to align the sequences in each homologous gene clustering group.
3. Use the software to screen for conserved regions of gene sequences.
4. Construct a maximum likelihood tree of the conserved sequences using the software.
5. Prune the single gene tree using the software to obtain a one-to-one matrix of direct homologs with only one sequence per taxon.

• Phylogenetic and Reticulate Evolutionary Analysis

Phylogenetic analyses were performed using tandem and concatenation analyses.

1. For the tandem matrices: (1) each screened direct homolog was compared using MUSCLE software to form a sequence matrix; (2) each matrix was screened for conserved regions using GBlock software; (3) the screened conserved sequence matrices were tandem to form a multigene supermatrix; (4) maximum likelihood analysis was performed using RAxML software. (4) maximum likelihood analysis using RAxML software.
2. The method of joint gene trees: (1) each direct homolog was analyzed individually by maximum likelihood using RAxML software; (2) the single gene trees were classified according to topology and the number of genes with different topologies was counted; (3) multiple single gene trees were combined into a supertree using ASTRAL software.

Applications

• Plant evolutionary analysis services are essential for understanding the development and evolution of plant embryos, vascular tissues, seeds, and flowers.
• Comparative genome-based bioinformatics analyses can elucidate both the vertical evolutionary processes of plant genes and the horizontal evolutionary processes of water.

Why Choose Lifeasible

With the rapid development of molecular biology, molecular data have become the main trait for phylogenetic analysis. However, as research progresses, phylogenetic trees from phylogenetic analyses of the same taxon using different gene sequences vary from one researcher to another. Our analysis service enables the use of phylogenetic networks to accurately reconstruct gene network relationships during the evolution of species.

How to Place an Order

Lifeasible provides a one-stop shop for plant phylogenetic and molecular evolutionary analysis, from sequencing to bioinformatics. Please contact us directly if you require further information.