Automated improvement of stickleback reference genome assemblies with Lep‐Anchor software

Abstract

Great deal of present-day research in biology is based on genomic data that are processed and analysed in the context of a linear reference genome. Typical examples of this are whole-genome sequencing studies where sequencing reads are mapped to the reference genome and the characteristics of interest are derived from local dissimilarities and statistics based on the alignments (Korneliussen et al., 2014;Schraiber & Akey, 2015). Reliability of those characteristics and the conclusions drawn from them depend not only on the quality of the sequencing data but also on the quality of the reference genome. Assembling and evaluating the quality of reference genomes is not easy (Baker, 2012;

Complex population history affects admixture analyses in nine‐spined sticklebacks

“…In addition, we exploited the information from the sex chromosomes, known to differ between the two evolutionary lineages (Natri et al, 2019 ), to gain additional information of the population origins. However, the WL sex determination locus is unknown and we could only identify the EL males (the heterogametic sex), expected to show a sequencing coverage ratio close to 0.5:1 across the sex‐chromosome and pseudo‐autosomal parts of LG12 (Figure S11 , Kivikoski et al, 2021 ).…”

HGGA: hierarchical guided genome assembler

“…We ran several experiments using simulated Caenorhabditis elegans reads and a simulated genetic linkage map, real Arabidopsis thaliana reads and simulated genetic linkage map, real human reads and a simulated genetic linkage map, and using real reads and a real genetic linkage map for an additional C. elegans data set [ 17 , 18 ] and a nine-spined stickleback Pungitius pungitius data set from a recent assembly project [ 19 , 20 ]. C. elegans , A. thaliana , and human have good quality reference genomes which allow us to evaluate the correctness of the produced assemblies accurately.…”

“…The A. thaliana reads are available at https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData . The P. pungitius reads were downloaded from ERA (accession code ERR3569182) and the genetic linkage map is from [ 20 ]. The Illumina reads of P. pungitius were also downloaded from ERA (accession codes ERR3618123 and ERR3618124).…”

Inbreeding depression in an outbred nine-spined stickleback (Pungitius pungitius) population

“…Individuals were placed at random to ensure that half of each family was represented in each aquarium. Offspring were mass-reared and their parental identity were subsequently recovered from genotype data as explained in [43] (and see below). Offspring survival was scored as the number of F 1 fish alive at the end of the experiment.…”

“…The fish used in this study came from a large crossing design used in previous studies [43]. Wild parental fish were caught from a marine population in the Baltic Sea in Finland (60°13’N, 25°11’E) and brought to the aquarium facility of the University of Helsinki.…”