Biology subjects

Schafran, P. W.

Publications and source records attributed to Schafran, P. W..

3 recordsLinked to original sources

bioRxiv2021

PURC v2.0: a program for improved sequence inference for polyploid phylogenetics and other manifestations of the multiple-copy problem

Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatic problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved upon by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs). To date, ASV approaches have been used primarily in metagenomics, but they are also useful for identifying allelic or paralogous variants and for determining homeologs in polyploid organisms. To facilitate the usage of ASV methods among polyploidy researchers, we incorporated ASV inference alongside OTU clustering in PURC v2.0, a major update to PURC (Pipeline for Untangling Reticulate Complexes). In addition to preserving original PURC functions, PURC v2.0 allows users to process PacBio CCS/HiFi reads through DADA2 to generate and annotate ASVs for multiplexed data, with outputs including separate alignments for each locus ready for phylogenetic inference. In addition, PURC v2.0 features faster demultiplexing than the original version and has been updated to be compatible with Python 3. In this chapter we present results indicating that PURC v2.0 (using the ASV approach) is more likely to infer the correct biological sequences in comparison to the earlier OTU-based PURC, and describe how to prepare sequencing data, run PURC v2.0 under several different modes, and interpret the output. We expect that PURC v2.0 will provide biologists with a method for generating multi-locus "moderate data" datasets that are large enough to be phylogenetically informative and small enough for manual curation.

bioinformatics↗

bioRxiv2020

Metagenomic characterization of a harmful algal bloom using nanopore sequencing

Water bodies around the world are increasingly threatened by harmful algal blooms (HABs) under current trends of rising water temperature and nutrient load. Metagenomic characterization of HABs can be combined with water quality and environmental data to better understand and predict the occurrence of toxic events. However, standard short-read sequencing typically yields highly fragmented metagenomes, preventing direct connection of genes to a single genome. Using Oxford Nanopore long-read sequencing, we were able to obtain high quality metagenome-assembled genomes, and show that dominant organisms in a HAB are readily identified, though different analyses disagreed on the identity of rare taxa. Genes from diverse functional categories were found not only in the most dominant genera, but also in several less common ones. Using simulated datasets, we show that the Flongle flowcell may provide an option for HAB monitoring with less data, at the expense of failing to detect rarer organisms and increasing fragmentation of the metagenome. Based on these results, we believe that Nanopore sequencing provides a fast, portable, and affordable method for studying HABs.

genomics↗

bioRxiv2020

Revealing the evolutionary history of a reticulate polyploid complex in the genus Isoëtes

O_LIPolyploidy and hybridization are important processes in the evolution of spore-dispersed plants. Few studies, however, focus these dynamics in heterosporous lycophytes, such as Isoetes, where polyploid hybrids are common and thought to be important in the generation of their extant diversity. We investigate reticulate evolution in a complex of western North American quillworts (Isoetes) and provide insights into the evolutionary history of hybrids, and the role of polyploidy in maintaining novel diversity. C_LIO_LIWe utilize low copy nuclear markers, whole plastomes, restriction site-associated DNA sequencing, cytology, and reproductive status (fertile or sterile) to investigate the reticulate evolutionary history of western North American Isoetes. C_LIO_LIWe reconstruct the reticulate evolutionary history and directionality of hybridization events in this complex. The presence of high level polyploids, plus frequent homoploid and interploid hybridization suggests that there are low prezygotic reproductive barriers in this complex, hybridization is common and bidirectional between similar--but not divergent--cytotypes, and that allopolyploidization is important to restore fertility in some hybrid taxa. C_LIO_LIOur data provide five lines of evidence suggesting that hybridization and polyploidy can occur with frequency in the genus, and these evolutionary processes may be important in shaping extant Isoetes diversity. C_LI

evolutionary biology↗