Global Diversity

Table 3.4: Estimated and observed global transcript diversity in M. truncatula root libraries. Global diversity ($S_{\gamma}$) is computed as the product of local (or alpha) and beta diversity ( $S_{\alpha} S_{\beta}$), summed over all libraries. Local diversity ($S_{\alpha}$) is the product of library diversity and the proportion of plant transcripts within a library, $P_{plant}$. Beta diversity is the mean complementarity compared with all other libraries, $\overline{C}$. Observed global diversity ($S_{net}$) is calculated in the same manner as $S_{\gamma}$, but substitutes observed local diversity ($S_{obs}$) for estimated ($\hat{S}$) in computing $S_{\alpha}$. Only diversity values from the 50% identity threshold are shown. Also shown are subtotals that exclude NF libraries from global diversity calculations.

LIBRARY	$\hat{S}$	$P_{plant}$	$\overline{C}$	$S_{\alpha} S_{\beta}$	$S_{obs}$	$S_{tot}$
MHAM	9053	0.773	0.918	6421	2311	1640
DSIR	8124	0.959	0.915	7130	1765	1549
KV0	8797	0.992	0.922	8047	1963	1795
KV3	9979	0.990	0.929	9182	1800	1655
SUBTOTAL	$S_{\gamma}=30780$				$S_{net}=6639$
NFroot	5554	0.996	0.943	5218	1636	1537
NFnod	9081	0.993	0.919	8287	2094	1911
TOTAL	$S_{\gamma}=44285$				$S_{net}=10087$

For a 50% identity threshold, estimated global diversity in the MHAM, DSIR, KV0, and KV3 libraries is 30,780 distinct transcripts (Table 3.4). If we include the NF root and nod libraries, estimated global diversity is 44,285. We note that beta diversity is the greatest unknown in these calculations. As noted above, complementarity calculations are based on observed diversity. Increasing samples should decrease complementarity between libraries, but at an unknown rate [32].

Our calculations for net observed diversity indicate more than 10,000 distinct M. truncatula root transcripts (Table 3.4) have resulted from nearly 15,000 samples analyzed in six different libraries.