Cadamomics (aka Neolamarkia cadamba EST database, NCdbEST)
The world first large scale genomic resource for wood formation in kelampayan (Neolamarkia cadamba) was successfully generated by a group of researchers from the Forest Genomics Laboratory (UNIMAS-SFC).
The world first large scale genomic resource for wood formation in kelampayan (Neolamarkia cadamba) was successfully generated by a group of researchers from the Forest Genomics Laboratory (UNIMAS-SFC). Cadamomics, also known as the Neolamarkia cadamba expressed sequence tags database (NCdbEST) contained 10,368 ESTs was generated through high-throughput 5’ EST sequencing of cDNA clones derived from developing xylem tissues.
Assembly of 6,622 high quality ESTs from 5’ end sequences generated 4,728 xylogenesis unigenes with an average length of 672 bp. The analysis formed 2,100 consensus contigs sequences (representing 3,994 or 60.3 % of the total high quality ESTs), with a length ranging from 132 bp to 2706 bp and an average length of 621 bp. The remaining 2,628 (representing 39.7 % of the total high quality ESTs) were singletons which ranged from 104 to 839 bp, with an average length of 723 bp. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in the GenBank. Assembly analysis revealed a redundancy level of 28.5% in the kelampayan EST database. By comparison, the EST redundancy in the kelampayan EST database is comparable to the estimated redundancy of 28 % in Populus and the 28.8 % in Pinus radiata.
The most abundant protein in the ESTs whose putative function was inferred from sequence comparison was 60s ribosomal protein with 92 ESTs, followed by 40s ribosomal protein with 42 ESTs. Interestingly, most genes involved in lignin biosynthesis were present in the kelampayan EST database with 1 to 21 ESTs. These include phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), coumarate 3-hydroxylase (ρ-coumaryl shikimate/quinate 3-hydroxylase) (C3H), caffeic acid O-methyltransferase (COMT), caffeoyl-CoA-3-O-methyltransferase (CCoAOMT), 4-coumarate:CoA reductase (4CL), ferulate 5-hydroxylase (F5H), cinnamyl alcohol dehydrogenase (CAD), hydroxycinnamoyl-CoA: shikimate/quinate hydroxycinnamoyl transferase (HCT) and cinnamoyl-CoA reductase (CCR). COMT, CCoAOMT and C3H are in the 30 highly abundant genes with 18 to 21 ESTs. Also, several ESTs exhibiting homologies to cell wall biosynthesis genes were also identified in the kelampayan EST database. The most highly abundant cell wall genes are tubulin (42 ESTs), arabinogalactan protein genes (30 ESTs) and cellulose synthase (13 ESTs). Other cell wall related genes including sucrose synthase, expansin, UDP-glucose dehydrogenase, xyloglucan endotransglycosylase and pectate lyase are moderately abundant with 2 to 11 ESTs in the kelampayan EST database.
This study has generated an important genomic resource for wood formation in kelampayan. The identified genes in this study will provide a useful resource for identifying molecular mechanisms controlling wood formation and will also be candidates for association genetic studies in kelampayan aiming at the production of high value forests. Furthermore, comparison of kelampayan ESTs with sequences from angiosperms will also generate valuable information about the evolution of higher plants.
Please feel free to visit us at CADAMOMICS for further information about the kelampayan EST project.