Transposable element subfamily annotation has a reproducibility problem.

Background: Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that are often intended to capture family history. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee.

Results: We find that standard methods annotate over 10% of replicates as belonging to different subfamilies, despite the fact that they are expected to be annotated as belonging to the same subfamily.

Splice-Aware Multiple Sequence Alignment of Protein Isoforms.

Multiple sequence alignment (MSA) is a classic problem in computational genomics. In typical use, MSA software is expected to align a collection of homologous genes, such as orthologs from multiple species or duplication-induced paralogs within a species. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need to create MSAs that more effectively accommodate isoforms.

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia.

Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species.