A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

Abstract

In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000 th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome.

Characterization of a Tigger1 element from the genome of the American mink (Neovison vison)

“…However, in light of the ancient age of this class of elements and the potential effects of accumulated mutations, including indels and nested insertions, by more recently active classes of repetitive elements on hybridization signal strength, our estimate of Tigger1 element abundance in the mink genome could best be viewed as a lower end value. This estimate is generally consistent, however, with the frequency of Tigger1 element sequences within the mink BES sequence space (Benkel et al, 2012), i.e. three Tigger1-specific elements were observed in 2.7 Mb of sequence where the haploid content of the mink genome is estimated at between 2 and 3 Gb.…”

“…A representative mink Tigger1 sequence was developed using a combination of information derived from BAC end sequences (BESs), long range-inverse PCR (LR-IPCR) products, and long range PCR (LR-PCR) amplicons as follows: 1) In a previous report, we described the construction of a BAC library for the American mink and the generation of BESs from six randomly selected 384-well plates (up to 2304 clones) of this library (see Benkel et al, 2012). Three of these BESs (GenBank accessions: FI903037, FI902999, and ET189538), one BES from each of three different BAC clones, showed compelling similarity to the human Tigger1 element sequence (GenBank accession U49973) based on a BLASTN comparison (Altschul et al, 1990).…”

The first draft reference genome of the American mink (Neovison vison)

“…For the two BAC-end sequence libraries, after filtering out clones where it was not possible to find both ends, we had 1,795 pairs of BES (BAC-end sequence) from black mink 30 and 833 pairs BES from the CHORI-231 BAC library 5 . The BESs were mapped to the genome assembly.…”

“…BWA men infers the reads orientation and the insert size during alignment and the properly paired reads were reported from SAMtools 64 flagstat. Two external BES (BAC-end sequence) libraries 5 , 30 were also used to check the correctness of the draft assembly. Firstly, the two BAC-ends of the same BAC clone were collected and renamed; BAC clones missing one of the end reads were removed.…”

70 years of research on the American mink (Neovison vison schreb., 1777) genetics - where are we now?

“…This can be seen in both the dynamic increase in zoogeographical range of the species, and in its effective adaptation to ecological niches in new areas (GENOVESI et al, 2010;SINITSYN, 1992;HALLIWELL and MACDONALD, 1996). Nevertheless, despite the increasing economic importance of the American mink and its wide geographical spread, the genome of this species remains one of the least studied among livestock species (ANISTOROAEI et al, 2009;BENKEL et al, 2012).…”