To reference this project in publications, please cite the following:

Bernhardsson, Carolina, Amaryllis Vidalis, Xi Wang, Douglas G. Scofield, Bastian Shiffthaler, John Baison, Nathaniel R. Street, M. Rosario Garcia Gil, and Pär K. Ingvarsson. 2018. “An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (*Picea abies*). *bioRxiv*. [https://doi.org/10.1101/292151](https://doi.org/10.1101/292151).

```
@UNPUBLISHED{Bernhardsson2018-jz,
   title    = "An ultra-dense haploid genetic map for evaluating the highly
              fragmented genome assembly of Norway spruce (Picea abies)",
   author   = "Bernhardsson, Carolina and Vidalis, Amaryllis and Wang, Xi and
              Scofield, Douglas G and Shiffthaler, Bastian and Baison, John and
              Street, Nathaniel R and Rosario Garcia Gil, M and Ingvarsson,
              P{\"a}r K",
   abstract = "Norway spruce (Picea abies (L.) Karst.) is a conifer species with
              large economic and ecological importance. As with most conifers,
              the P. abies genome is very large (~20 Gbp) and contains high
              levels of repetitive DNA. The current genome assembly (v1.0)
              covers approximately 60\% of the total genome size, but is highly
              fragmented consisting of more than 10 million scaffolds. Even
              though 66,632 protein coding gene models are annotated, the
              fragmented nature of the assembly means that there is currently
              little information available on how these genes are physically
              distributed over the 12 P. abies chromosomes. By creating an
              ultra-dense genetic linkage map, we can anchor and order
              scaffolds at the pseudo-chromosomal level in P. abies, which
              complements the fine-scale information available in the assembly
              contigs. Our ultra dense haploid consensus genetic map consists
              of 15,005 markers from 14,336 scaffolds and where 17,079 gene
              models (25.6\% of protein coding gene annotations) have been
              anchored to the 12 linkage groups (pseudo-chromosomes). Three
              independent component maps, as well as comparisons to earlier
              published Picea maps are used to evaluate the accuracy and marker
              order of the linkage groups. We can demonstrate that
              approximately 3.8\% of the scaffolds and 1.6\% of the gene models
              covered by the consensus map are likely wrongly assembled as they
              contain genetic markers that map to different regions or linkage
              groups of the P. abies linkage map. We also evaluate the utility
              of the genetic map for the conifer research community by using an
              independent data set of unrelated individuals to assess
              genome-wide variation in genetic diversity using the genomic
              regions anchored to chromosomes. The results show that our map is
              dense enough to allow detailed evolutionary analysis across the
              P. abies genome.",
  journal  = "bioRxiv",
  pages    = "292151",
  month    =  apr,
  year     =  2018,
  language = "en"
}