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Fig. 2 | BMC Biology

Fig. 2

From: Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Fig. 2

Improved genome assemblies for 20 anophelines from solely synteny-based scaffold adjacency predictions. Results from ADseq, Gos-Asm, and OrthoStitch predictions were compared to define two-way consensus adjacencies predicted by at least two of the three approaches, where the third approach did not conflict. These adjacencies were used to build new assemblies with improved contiguities, quantified by comparing before and after scaffold counts and N50 values (half the total assembly length comprises scaffolds of length N50 or longer). The counts, values, and ratios represent only scaffolds with annotated orthologous genes used as the input dataset for the scaffold adjacency predictions. To make the N50s before and after superscaffolding directly comparable, the values for the new assemblies do not include the 100 Ns used to join scaffold adjacencies. a Scaffold counts (blues, bottom axis) and N50 values (red/orange, top axis) are shown before (dots) and after (arrowheads) synteny-based improvements were applied. The 20 anopheline assemblies are ordered from the greatest N50 improvement at the top for Anopheles dirus to the smallest at the bottom for Anopheles albimanus. Note axis scale changes for improved visibility after N50 of 5 Mbp and scaffold count of 6000. b Plotting before to after ratios of scaffold counts versus N50 values (counts or N50 after/counts or N50 before superscaffolding of the adjacencies) reveals a general trend of a ~ 33% reduction in scaffold numbers resulting in a ~ 2-fold increase of N50 values. The line shows the linear regression with a 95% confidence interval in grey. Results for two strains are shown for Anopheles sinensis, SINENSIS and Chinese (C), and Anopheles stephensi, SDA-500 and Indian (I)

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