Table 4

Analysis of transcriptome complexity

RCC1217 1N

RCC1216 2N

Combined libraries


Total clusters

7,887

8,688

13,056

ML estimate of transcriptome richness

10,039

11,988

16,211

Chao1 ± SD (boundaries of 95% CI)

12,840 ± 214 (12,438, 13,278)

15,931 ± 289 (15,385, 16,522)

22,169 ± 314 (21,573, 22,806)

Coverage (%) based on richness estimates

61.4-78.6

54.5-72.5

58.9-80.5

Shannon diversity (maximum possible)

8.66 (8.97)

8.76 (9.06)

9.05 (9.48)


The maximum likelihood (ML) estimate of transcriptome richness was calculated following Claverie [23] using the two separate rounds of EST sequencing. The Chao1 estimator of transcriptome richness and the Shannon diversity index was computed for each library separately and for the combined library using EstimateS with the classic formula for Chao1. The range of estimated coverage was calculated by dividing the number of clusters observed by the two estimates of transcriptome richness. The similarity of content of the 1N and 2N libraries was also determined: the Chao abundance-based estimator of the Jaccard similarity index (accounting for estimated proportions of unseen shared and unique transcripts) was 0.506 ± 0.009, calculated with 200 bootstrap replicates and the upper abundance limit for rare or infrequent transcript species set at 2. The maximum possible Shannon diversity index was calculated as the natural log of the number of clusters.

von Dassow et al. Genome Biology 2009 10:R114   doi:10.1186/gb-2009-10-10-r114

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