High-throughput sequencing of a single chromosome: a moth W chromosome.
Y and W chromosomes have mostly been excluded from whole genome sequencing projects. Due to the high amount of repetitive sequences they are 'difficult' to assemble and therefore need special treatment in the form of, e.g. adapted assembly programs, a range of different libraries, and accurate maps, if possible. A minimum requirement for these approaches is pure template DNA. We therefore microdissected the W chromatin of highly polyploid cells from the flour moth, Ephestia kuehniella, and used Roche/454 and Sanger sequencing to generate 72.6 Mbp of DNA sequence. Nominal coverage was 4.3× of the 16.7 Mbp of W chromosomal DNA. We used these data to assess the genetic content of the W chromosome. This approach allowed us to determine constituent families of transposable elements, microsatellites, and recent insertion sites of mitochondrial DNA. However, no conventional protein-coding gene has yet been found. The sequence collection is a rich source for the definition of W-specific PCR markers and the reconstruction of W chromosome loci, as a step towards full reconstruction of the chromosome.
Zentrum für Medizinische Strukturbiologie, Institut für Biologie, Universität Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany. traut@bio.uni-luebeck.de
Walther
W
Traut
Heiko
H
Vogel
Gernot
G
Glöckner
Enno
E
Hartmann
David G
DG
Heckel
D000818:Animals; D001483:Base Sequence; D020223:Chromosome Painting; D059006:Chromosomes, Insect; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D004272:DNA, Mitochondrial; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D018895:Microsatellite Repeats; D009036:Moths / Q000235:genetics*; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D012730:Sex Chromosomes
D004251:DNA Transposable Elements; D004272:DNA, Mitochondrial