PMID- 19573234
OWN - NLM
STAT- MEDLINE
DCOM- 20090804
LR  - 20211020
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 10
DP  - 2009 Jul 2
TI  - A BAC-based physical map of the Hessian fly genome anchored to polytene 
      chromosomes.
PG  - 293
LID - 10.1186/1471-2164-10-293 [doi]
AB  - BACKGROUND: The Hessian fly (Mayetiola destructor) is an important insect pest of 
      wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 
      Mb). Investigation of the Hessian fly presents excellent opportunities to study 
      plant-insect interactions and the molecular mechanisms underlying genome 
      imprinting and chromosome elimination. A physical map is needed to improve the 
      ability to perform both positional cloning and comparative genomic analyses with 
      the fully sequenced genomes of other dipteran species. RESULTS: An FPC-based 
      genome wide physical map of the Hessian fly was constructed and anchored to the 
      insect's polytene chromosomes. Bacterial artificial chromosome (BAC) clones 
      corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, 
      using high information content fingerprinting (HIFC) methodology, and 
      end-sequenced. Fluorescence in situ hybridization (FISH) co-localized two BAC 
      clones from each of the 196 longest contigs on the polytene chromosomes. An 
      additional 70 contigs were positioned using a single FISH probe. The 266 FISH 
      mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). 
      The ends of the fingerprinted BACs were then sequenced to develop the capacity to 
      create sequenced tagged site (STS) markers on the BACs in the map. Only 3.64% of 
      the BAC-end sequence was composed of transposable elements, helicases, ribosomal 
      repeats, simple sequence repeats, and sequences of low complexity. A relatively 
      large fraction (14.27%) of the BES was comprised of multi-copy gene sequences. 
      Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs). 
      CONCLUSION: This physical map provides the foundation for high-resolution genetic 
      mapping, map-based cloning, and assembly of complete genome sequencing data. The 
      results indicate that restriction fragment length heterogeneity in BAC libraries 
      used to construct physical maps lower the length and the depth of the contigs, 
      but is not an absolute barrier to the successful application of the technology. 
      This map will serve as a genomic resource for accelerating gene discovery, genome 
      sequencing, and the assembly of BAC sequences. The Hessian fly BAC-clone 
      assembly, and the names and positions of the BAC clones used in the FISH 
      experiments are publically available at 
      (http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/).
FAU - Aggarwal, Rajat
AU  - Aggarwal R
AD  - Department of Entomology, Purdue University, West Lafayette, IN 47907, USA. 
      raggarw@purdue.edu
FAU - Benatti, Thiago R
AU  - Benatti TR
FAU - Gill, Navdeep
AU  - Gill N
FAU - Zhao, Chaoyang
AU  - Zhao C
FAU - Chen, Ming-Shun
AU  - Chen MS
FAU - Fellers, John P
AU  - Fellers JP
FAU - Schemerhorn, Brandon J
AU  - Schemerhorn BJ
FAU - Stuart, Jeff J
AU  - Stuart JJ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20090702
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
SB  - IM
MH  - Animals
MH  - Chromosome Walking
MH  - Chromosomes, Artificial, Bacterial/genetics
MH  - Contig Mapping/*methods
MH  - DNA Fingerprinting/methods
MH  - Diptera/*genetics
MH  - *Genome, Insect
MH  - Genomic Library
MH  - In Situ Hybridization, Fluorescence
MH  - Sequence Analysis, DNA/methods
PMC - PMC2709663
EDAT- 2009/07/04 09:00
MHDA- 2009/08/06 09:00
PMCR- 2009/07/02
CRDT- 2009/07/04 09:00
PHST- 2009/01/13 00:00 [received]
PHST- 2009/07/02 00:00 [accepted]
PHST- 2009/07/04 09:00 [entrez]
PHST- 2009/07/04 09:00 [pubmed]
PHST- 2009/08/06 09:00 [medline]
PHST- 2009/07/02 00:00 [pmc-release]
AID - 1471-2164-10-293 [pii]
AID - 10.1186/1471-2164-10-293 [doi]
PST - epublish
SO  - BMC Genomics. 2009 Jul 2;10:293. doi: 10.1186/1471-2164-10-293.