Fig. 4

Identification and characterization of Rosaceae-common potential coding gene. a Venn diagram shows the Rosaceae-common and Rosa-specific transcripts. Note that, except Rosa, transcripts specific for other genera were not identified (marked with na). For that we are not interested in other share sets. b GO enrichment analysis of the 4447 Rosaceae-common transcripts (http://bioinfo.cau.edu.cn/agriGO). X-axis shows the enrichment fold of specific GO terms in comparison with the background. BP, CC and MF mean biological process, cellular component and molecular function separately. The area indicates gene counts. c Representive phylogentic topologies based on 4447 Rosaceae-common genes. Upper panel indicates about 65% topologies (2812) supporting the clustering of Prunus with Malus, while the topology in lower panel is supported by 33% genes (1436). Numbers on branches indicate distance. d Three-dimensional plots for the genetic distances of the 4447 transcripts between Rosa and Fragaria (X-axis) /Malus (Y-axis) /Prunus (Z-axis). Black and blue dots mark the genes supporting the topologies in C (Black for upper panel and blue for lower panel), while gray dots show genes supporting other topologies. e Distribution and GO enrichment analysis of the 409 selected Rosaceae-common transcripts. Y-axis shows the enrichment fold of specific GO terms in comparison with the background. Only four GO items are significantly enriched (marked in orange color). f Clustered heat map comparing scaled expression values for the 409 selected Rosaceae-common transcripts. Yellow indicates higher while purple marks lower expression. Blue and red bars indicate membership in the identified transcription clusters