ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data.

SUMMARY: Exitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for the detection and annotation of exitrons in long-read RNA-seq data. Here, we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the individual transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. In addition, ScanExitronLR optionally reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data. AVAILABILITY AND IMPLEMENTATION: ScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A new ankylosaurid dinosaur from the Upper Cretaceous (Kirtlandian) of New Mexico with implications for ankylosaurid diversity in the Upper Cretaceous of western North America.

A new ankylosaurid (Ankylosauria: Dinosauria), Ziapelta sanjuanensis, gen. et sp. nov., is based on a complete skull, an incomplete first cervical half ring, a possible fragment of the second cervical half ring, and additional fragmentary osteoderms. The holotype specimen is from the Upper Cretaceous (Upper Campanian, Kirtlandian Land-Vertebrate Age) Kirtland Formation (De-na-zin Member) at Hunter Wash, San Juan Basin, in northwestern New Mexico, USA. Diagnostic characters of Ziapelta include: a large, prominent triangular median nasal caputegulum; a mixture of flat and bulbous frontonasal caputegulae; ventrolaterally oriented squamosal horns with a sharp, prominent dorsal keel; and the ventral surface of basicranium with three prominent anteroposteriorly oriented fossae. A phylogenetic analysis suggests that Ziapelta is not closely related to the other ankylosaurid from the De-na-zin Member, Nodocephalosaurus, but allies it to the northern North American ankylosaurids Ankylosaurus, Anodontosaurus, Euoplocephalus, Dyoplosaurus, and Scolosaurus.