Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development

Abstract

Vertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized. In this study, we applied high-throughput sequencing on the transcriptomes of 13 developmental stages of Chinese amphioxus to gain a comprehensive understanding of transcriptional processes occurring from the fertilized egg to the adult stage. The expression levels of 3,423 genes were significantly changed (FDR ≤ 0.01). All of these genes were included in a clustering analysis, and enrichment of biological functions associated with these clusters was determined. Significant changes were observed in several important processes, including the down-regulation of the cell cycle and the up-regulation of translation. These results should build a foundation for identifying developmentally important genes, especially those regulatory factors involved in amphioxus development, and advance understanding of the developmental dynamics in vertebrates.

Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates

“…4). In addition, amphioxus Hox6-15 genes might still follow WTC at later stages than the ones assayed here 37 A more detailed investigation of the temporal expression of Hox genes in non-chordate deuterostome groups (namely, ambulacrarians -e.g., sea urchins, sea stars, acorn worms-) will be thus needed to ultimately resolve this question 40,41 .…”

“…Expression profiles of Hox genes in the cephalochordate amphioxus Branchiostoma belcheri 37 show that amphioxus Hox1 to Hox5 are expressed in an anterior Hox/earlyposterior/late manner. However, Hox6, Hox10 and Hox14 genes violate this pattern, consistent with our previous report 38 , and Hox7-8, Hox11-13 and Hox15 were not detected during the stages assayed, contributing to the dismantling of the colinearity (Fig.…”

“…TPM values from either genes (for Hox genes represented with a single transcript in the assemblies) or isoforms (for Hox genes represented with several transcripts)were then selected and a heat map analyses of the log(TPM+0.1) were conducted in R using heatmap.2 (gplots package73 ) scaling by gene (row Z-score), and implemented in RStudio v1.0.13674 [with R v3.3.0 (2016-05-03)75 ]. B. belcheri Hox transcripts were quantified using previously published DGE-seq data37 with DGE-EM v1.0.0 76 software, and FPKM values were analysed as above.…”

Characterization of an amphioxus heat-shock protein gene promoter and its application in vivo

“…In Xenopus, the earliest stage when Hsp70 can be induced by heat shock corresponds to the stage when zygotic gene expression is activated (Lang et al, 2000). This is probably the same case in amphioxus, since heat-shock-induced Hsp70 mRNA was detected only from the 128-cell stage on, when the zygotic genome is thought to be activated (Yang et al, 2016). Lastly, as it is in zebrafish (Lele et al, 1997) and Xenopus embryos (Lang et al, 2000), the induced Hsp70 expression level by heat shock in amphioxus embryos is not identical among different tissues.…”

Single cell chromatin accessibility of the developmental cephalochordate

“…Yang et al performed RNAseq for Branchiostome, covering 13 development stages, ranging from fertilized egg to adults. In total, they identified 3423 genes changed significantly during the development, including the increase of translation associated genes and decrease of cell cycle genes 5 . Marletaz et al performed whole genome sequencing for Branchiostome lanceolatum and constructed genomic profiles including transcriptome, histone modification, DNA methylation and chromatin accessibility at bulk level.…”