SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism.
Super-serial analysis of gene expression (SuperSAGE) was used to characterize, for the first time, the global gene expression pattern in banana (Musa acuminata). A total of 10,196 tags were generated from leaf tissue, representing 5,292 expressed genes. Forty-nine tags of the top 100 most abundantly expressed transcripts were annotated by homology to cDNA or EST sequences. Typically for leaf tissue, analysis of the transcript profiles showed that the majority of the abundant transcripts are involved in energy production, mainly photosynthesis. However, the most abundant tag was derived from a type 3 metallothionein transcript, which accounted for nearly 3% of total transcripts analysed. Furthermore, the 26-bp long SuperSAGE tags were applied in 3'-rapid amplification of cDNA ends (3'RACE) for the identification of unknown tags. In combination with thermal asymmetric interlaced PCR (TAIL-PCR), this allowed the recovery of a full gene sequence of a novel NADPH:protochlorophyllide oxidoreductase, the key enzyme in chlorophyll biosynthesis. SuperSAGE in conjunction with 3'RACE and TAIL-PCR will be a powerful tool for transcriptomics of non-model, but otherwise important organisms.
Coemans
Bert
B
Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, 3001 Leuven, Belgium. bert.coemans@agr.kuleuven.ac.be
Matsumura
Hideo
H
Terauchi
Ryohei
R
Remy
Serge
S
Swennen
Rony
R
Sági
László
L
D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D008969:Molecular Sequence Data; D028521:Musa / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D018076:DNA, Complementary; D044925:Oxidoreductases Acting on CH-CH Group Donors; C023886:protochlorophyllide reductase