EST and transcriptome analysis of cephalochordate amphioxus--past, present and future

Abstract

The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.

Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data

“…For our identified B. floridae germline cell development-related gene models, we located the available ESTs/cDNA information in both the B. floridae cDNA database and the NCBI EST database (Wang et al, 2012;Yu et al, 2008). Using the protein sequence of the corresponding B. floridae gene models, we performed a TBLASTN search using an e-value cutoff of 1E-6.…”

Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates

“…Such organisms include the amphioxus ( Branchiostoma floridae ), which has recently been suggested to be the basal chordate clade [28-31]. Studies on amphioxus have been facilitated by the sequencing of its genome and by the available cDNA and EST resources [28,32-34]. Previous surveys based on gene models predicted the existence of nine families of bHLH-PAS genes in amphioxus, but experimental validation of transcripts and the expression patterns of these genes were lacking [4,11].…”