Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics

Abstract

Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq), in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs) were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

Keywords: Gene expression; Heterophyllous leaves; Potamogeton octandrus; Transcriptome.

Figure 1. Morphological features of P. octandrus.

(A) The initial developmental stage of the plant that produces only submerged leaves. (B) The later developmental stage of the plant that produces both floating and submerged leaves.

Figure 2. Gene ontology (GO) annotations of all detected genes.

Three main categories including “biological process”, “cellular component”, and “molecular function” were summarized.

Figure 3. DEGs identified in comparisons among different P. octandrus leaf development stages.

“T01, T04, T12”, “T02, T03, T05”, “T06, T08, T13”, “T07, T10, T14”, and “T08, T11, T15” indicate three biological replicates of shoot, juvenile floating leaves, adult floating leaves, juvenile submerged leaves, and adult submerged leaves, respectively. (A) Venn diagram showing common and unique DEGs among different comparisons of floating leaves. (B) Venn diagram showing common and unique DEGs among different comparisons of submerged leaves. (C) Expression patterns of DEGs among different comparisons. The numbers above each bar indicate the total number of genes in each group.

Figure 4. GO functional classifications of DEGs identified from comparisons among different groups during floating leaf development.

“T01, T04, T12”, “T02, T03, T05”, and “T06, T08, T13” indicate three biological replicates of shoot, juvenile floating leaves, and adult floating leaves, respectively.

Figure 5. GO functional classifications of DEGs identified from comparisons among different groups during submerged leaf development.

“T01, T04, T12”, “T07, T10, T14”, and “T08, T11, T15” indicate three biological replicates of shoot, juvenile submerged leaves, and adult submerged leaves, respectively.

Figure 6. Dendrogram showing similarities in transcription factor expression profiles among samples.

Three transcription factor cluster groups (G1, G2 and G3) resulted from the 469 significantly differentially expressed transcription factors in leaves from different stages of development.

Figure 7. Distribution of transcription factor families among the three transcription factor cluster groups (G1, G2 and G3).