Improving PacBio Long Read Accuracy by Short Read Alignment

The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies. Here we present a computational method, LSC, to perform error correction of TGS long reads (LR) by SGS short reads (SR). Aiming to reduce the error rate in homopolymer runs in the main TGS platform, the PacBio® RS, LSC applies a homopolymer compression (HC) transformation strategy to increase the sensitivity of SR-LR alignment without scarifying alignment accuracy. We applied LSC to 100,000 PacBio long reads from human brain cerebellum RNA-seq data and 64 million single-end 75 bp reads from human brain RNA-seq data. The results show LSC can correct PacBio long reads to reduce the error rate by more than 3 folds. The improved accuracy greatly benefits many downstream analyses, such as directional gene isoform detection in RNA-seq study. Compared with another hybrid correction tool, LSC can achieve over double the sensitivity and similar specificity.     

Analysis of cell movements and fate mapping during early embryogenesis in Drosophila melanogaster

Four spatially differentiated surface regions, called aeropyle crown, flat, stripe, and micropyle, are found on the mature eggshell (chorion). Specializations of the apical surfaces of the secretory follicular epithelial cells are implicated in the formation of regional patterns on the chorion. Some of these specializations are restricted to cells overlying certain regions; others are shared by more than one region. Differences between regions are more apparent on the surface than within the bulk of the chorion. Evidence is presented that distinct cell populations, corresponding to the regions, are present long before the start of choriogenesis. One hundred eighty-six chorion-specific polypeptides have been resolved by two-dimensional gel electrophoresis. Fifteen of these are found entirely or predominantly in the aeropyle crown and stripe regions, while eight others are restricted to the aeropyle crown region. Certain of the spatially restricted components are quite unusual in their amino acid compositions when compared with previously analyzed chorion components. Others are closely related, although clearly distinct.     

Shark and ray teeth from the Hauterivian (Lower Cretaceous) of north-east England

Sampling of hiatal horizons within the Hauterivian part of the Speeton Clay Formation of north-east England has produced teeth of several species of sharks and rays, four of which are previously unnamed. One species of shark, Cretorectolobus doylei sp. nov., and two species of rays, Spathobatis rugosus sp. nov. and Dasyatis speetonensis sp. nov., are named, whilst the presence of an indeterminate triakid shark is also noted. Synechodus dubrisiensis (Mackie) is shown to be a senior synonym of S. michaeli Thies. Although the dasyatid ray and triakid shark are by far the oldest representatives of their respective families, the overall composition of the fauna is considered to resemble more closely assemblages known from the Jurassic than those from upper parts of the Cretaceous.     

A method for analysing spatial scales of variation in composition of assemblages

In several areas of research on ecological assemblages, it is useful to be able to analyse patterns of spatial variation at various scales. Multivariate analyses of dissimilarity or similarity in assemblages of species are limited by problems of non-independence caused by repeated use of the sample-units. Where rank-order procedures are used, no comparative quantitative measurements of dissimilarity at different scales are produced. An alternative method is described that uses the sample's average assemblage (or centroid). These estimates are themselves averaged to give centroids for larger spatial scales. Dissimilarities from the centroids at each scale are then calculated using independent replicates for each scale from those in each sample. The dissimilarity measures can then be examined by analysis of variance to detect spatial scales of differences for each sample at every level of a hierarchy of scales. The method is illustrated using data from mangrove forests and rocky shores, involving up to 97 taxonomic groups (species, other taxa). Differences among assemblages at the scales of sites (tens of meters apart) or locations at shores (hundreds of meters apart) were identified. Consequences of different numbers of replicates are discussed, with some potential problems (and their solutions) in application. Received: 14 November 1997 / Accepted: 14 September 1998