Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

Table 1 Summary of de novo assemblies and BLASTn results for Illumina and 454 genomes

	Illumina (159,514) bp)		454 (159,382 bp)
	CLC	Velvet	CLC	Newbler
Total number of contigs	171 603	278	126	39
Mean contig length	261	769	1 565	5 518
Longest contig	49 987	13 879	20 405	33 064
N50	252	3 049	4 065	18 420
Number of chloroplast contigs (E value = 0)*	12	33	24	11
Longest chloroplast contig	33 886	12 240	20 405	33 060
Sum (bp) of chloroplast contigs	146 401	129 686	132 317	132 215
Chloroplast reads (% of total reads) **	5.25%		99.00%

Genbank accession numbers for the 80 contigs GenBank:JX445406 – Jx445485.
*determined by a BLASTn search against a database of 134 whole chloroplast genomes downloaded from GenBank.
**determined by mapping the total reads onto the whole chloroplast genome for Toona ciliata in CLC with default settings.

ISSN: 1472-6785