De novo transcriptome sequencing and analysis of Hydrilla verticillata (L.f.) Royle

Abstract

Hydrilla verticillata (L.f.) Royle, an aquatic plant, best documented example of an inducible C4 photosynthetic system, which concentrates CO2 in the chloroplasts without enzymatic compartmentation in mesophyll and bundle sheath cells. H. verticillata is a facultative C4 plant, which shifts from C3 to C4 photosynthesis under certain conditions, but lacks Kranz anatomy. Little is known about the molecular changes required for the transition to the C4 carbon concentrating mechanism (CCM). To gain insight into the processes that are involved in the C3 to the C4 transition, high throughput transcriptome sequencing and analysis were carried out using 454-GS FLX Titanium technology. A total of 533,595 reads were obtained after quality filtering. From these reads, 1,813 “Expressed sequence tags (ESTs)” were generated yielding 1,538 unigenes. Almost 95% of these unigenes aligned to the “Nonredundant (nr)” database, whereas 4.88% did not show homology to any other known gene. “Reads per kilobase per million sequenced reads (RPKM)” analysis indicated that 283 unigenes were up-regulated and 383 unigenes were down-regulated in the C4 state as compared to the C3 state. A number of transcription factors found in our study were involved in photosynthesis. These consisted of, HAP3/NF-YB, AP/EREBP and C2H2 family. GO, COG and KEGG analysis indicated that many genes were involved in energy metabolism, nucleotide metabolism, photosynthesis, signal transduction, stress responses and are worthy of further investigation. This transcriptome analysis is an important first step towards understanding the molecular changes underpinning the transition from the C3 to the C4 photosynthesis in H. verticillata. It could also be a useful genomic resource for engineering C4 photosynthetic CCM in C3 crops.