December
2006
, Volume
19
, Number
12
Pages
1,302
-
1,310
Authors
Xuemin
Zhang
,
1
Chantel
Scheuring
,
2
Sucheta
Tripathy
,
1
Zhanyou
Xu
,
2
Chengcang
Wu
,
2
Angela
Ko
,
1
S. Ken
Tian
,
1
Felipe
Arredondo
,
1
Mi-Kyung
Lee
,
2
Felipe A.
Santos
,
2
Rays H. Y.
Jiang
,
1
Hong-Bin
Zhang
,
2
and
Brett M.
Tyler
1
Affiliations
1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, 24061-0477, U.S.A.; 2Department of Soil and Crop Sciences, Texas A&M University, College Station 77843-2474, U.S.A.
Go to article:
RelatedArticle
Accepted 24 July 2006.
Abstract
Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.
JnArticleKeywords
Additional keywords:
BAC end sequencing (BES)
,
BAC fingerprinting
.
Page Content
ArticleCopyright
© 2006 The American Phytopathological Society