Figure 1

Overview of the transcriptome of amphioxus.

(A) Distribution of the abundance of transcripts and the length of encoded proteins. The abundance of transcripts was calculated as FPKM with un-normalized RNA-Seq data. Transcripts that code for transcription factors are highlighted in red. (B) Heatmap showing expression patterns of top 20 highly expressed transcripts. Gene names are coloured according to their functions: red, ribosomal proteins; green, histone; black, hypothetical proteins. Values after gene names indicate the FPKM, which was estimated by Tophat-Cufflinks with un-normalized RNA-Seq data. Because they lacked a restriction site for the restriction enzyme NlaIII, the expression levels of several transcripts were not detectable across all stages by using DGE-Seq. a-m represent different developmental stages: a. egg, b. 2 cells, c. 16 cells, d. 64 cells, e. 128–256 cells, f. gastrula, g. neurula, h. hatch, i. 12 hours after hatching, j. 24 hours, k. 48 hours, l. male adult and m. female adult. (C) Features of a potential novel protein encoded by the transcript with highest expression level. Upper panel: alignment of RNA-Seq data on the amphioxus genome. Middle panel: pairwise alignment results of this protein with its counterpart in B. floridae. Lower panel: Domain structure of this protein.