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.

For the sake of consistency, we constructed transcriptome assemblies using our own pipeline, even in the cases where authors made assemblies publicly available. Briefly, our pipeline consisted of removing adapter sequences with Trimmomatic (39), followed by using two of the most popular transcriptome assemblers, the De Bruijn graph-based Trinity (40) and Trans-ABySS (41) Each species analyzed in this study, along with basic information concerning data type (genomic or transcriptomic), the number of genes here placed in orthologous gene sets, the N50 statistic (50% of bases are in contigs of length at least N50), and guanine-cytosine content (%GC) of these genes. For bats with transcriptomic data, data were all assembled and annotated as part of this study, and the number of assemblies constructed and analyzed is listed. For the other species, genomic data and annotations were all downloaded from RefSeq. Transcriptome data for two species, shown with asterisks, were generated in this study. assemblers, with a range of input parameters. This resulted in multiple tentative assemblies per bat (Table 1 and Methods) (39) (40) (41) (42) .