Phylogenetic inference using transcriptomic data
Method of phylogenetics
In molecular phylogenetics, relationships among individuals are determined using character traits, such as DNA, RNA or protein, which may be obtained using a variety of sequencing technologies. High-throughput next-generation sequencing has become a popular technique in transcriptomics, which represent a snapshot of gene expression. In eukaryotes, making phylogenetic inferences using RNA is complicated by alternative splicing, which produces multiple transcripts from a single gene. As such, a variety of approaches may be used to improve phylogenetic inference using transcriptomic data obtained from RNA-Seq and processed using computational phylogenetics.
Sequence acquisition
There have been several transcriptomics technologies used to gather sequence information on transcriptomes. However the most widely used is RNA-Seq.
RNA-Seq
RNA reads may be obtained using a variety of RNA-seq methods.
Public databases
There are a number of public databases that contain freely available RNA-Seq data.
Assembly
Sequence assembly
RNA-Seq data may be directly assembled into transcripts using sequence assembly.
Two main categories of sequence assembly are often distinguished:
de novo transcriptome assembly - especially important when a reference genome is not available for a given species.
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