A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

In summary, we have provided a way to combine genomic and transcriptomic data to build reliable multiple sequence alignments. We have created multiple sequence alignments for bat genes and made them publicly available. We have used these to produce a phylogeny and to assess positive selection in bat genes. Despite this progress, bats will continue to present challenges that push the limits of genomics and phylogenetics because of their high levels of sequence divergence. Data Cleaning and Assembly. Sequencing data were first cleaned to remove sequencing adaptors and low-quality bases with Trimmomatic (39), with appropriate settings for each dataset. Trinity (40) was run with all reads, with all reads with in silico normalization, and with ∼35 million read subsamples for those bats with large datasets as recommended in Francis et al. (95) . Trans-ABySS (41) was run with k-mer lengths of 32, 64, and all multiples of 5 from 25 to 60.