Skip to main content
Figure 1 | BMC Genomics

Figure 1

From: Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

Figure 1

Schematic of clone selection and complete insert sequencing of 4,664 FLcDNAs. CAP3 assembly of 90,368 high-quality 3'-end ESTs identified 35,011 putative unique transcripts (PUTs) for the identification of candidate FLcDNAs. Only those PUTs containing at least one clone from a FLcDNA library were considered further. To maximize the number of FLcDNAs captured, candidate clones were excluded from further analysis if: (1) the 5' second strand primer adaptor (SSPA) was absent; (2) a polyA tail was absent; (3) 5'- and/or 3'-end ESTs had a Phred20 quality length (Q20) of < 100 nt; or (4) BLASTN (E < 1e-80) versus poplar ESTs in the public domain identified a candidate as potentially truncated (i.e., > 100 nt shorter) at the 5' end of the transcript relative to a matching EST. Among the 5,926 candidates selected for sequencing, only 483 (8%) were aborted at various stages of the sequence finishing pipeline due to: (1) missing cloning structures; (2) errors in re-array of glycerol stocks; (3) problematic sequencing such as hard stops; or (4) problematic clone features such as chimeric sequences. Through a combination of end reads and gap closing using primer walking, 4,664 (79%) sequence-verified FLcDNAs were completed. An additional 779 clones (13%) from the starting set of 5,926 will be finished in future work.

Back to article page