Bản Đồ Tích Hợp Thế Hệ Thứ Hai của Bộ Gen Cá Câu Cầu Vồng (Oncorhynchus mykiss): Phân Tích Sự Bảo Tồn Synteny với Bộ Gen Của Các Loài Cá Mô Hình

Springer Science and Business Media LLC - Tập 14 - Trang 343-357 - 2011
Yniv Palti1, Carine Genet2, Guangtu Gao1, Yuqin Hu3, Frank M. You3,4, Mekki Boussaha2, Caird E. Rexroad1, Ming-Cheng Luo3
1National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, USA
2INRA, UMR1313, Génétique Animale et Biologie Intégrative, Jouy en Josas Cedex, France
3Department of Plant Sciences, University of California, Davis, USA
4Cereal Research Center, Agriculture and Agri-Food Canada, Winnipeg, Canada

Tóm tắt

Thông tin dấu vân tay DNA và chuỗi cuối từ các nhiễm sắc thể nhân tạo (BAC) từ hai thư viện mới đã được tạo ra để cải thiện bản đồ vật lý và di truyền thế hệ đầu tiên của bộ gen cá cầu vồng (Oncorhynchus mykiss). Phiên bản hiện tại của bản đồ vật lý bao gồm 167,989 dòng clone, trong đó 158,670 được lắp ráp thành các contig và 9,319 là đơn lẻ. Số lượng contig đã giảm từ 4,173 xuống 3,220. Việc định trình chuỗi cuối của các dòng clone từ các thư viện mới đã tạo ra tổng cộng 11,958 chuỗi trình tự chất lượng cao. Các chuỗi cuối này đã được sử dụng để phát triển 238 microsatellite mới, trong đó 42 được thêm vào bản đồ di truyền. Sửa đổi synteny bảo tồn giữa bộ gen cá cầu vồng và các bộ gen của các loài cá mô hình đã được phân tích bằng cách sử dụng 188,443 đọc chuỗi cuối BAC (BES). Tỉ lệ đọc BES có kết quả BLASTN đáng kể so với bộ gen cá đuối, medaka và stickleback lần lượt là 8.8%, 9.7%, và 10.5%, trong khi tỉ lệ kết quả BLASTX đáng kể so với cơ sở dữ liệu protein của cá đuối, medaka, và stickleback lần lượt là 6.2%, 5.8%, và 5.5%. Tổng số khu vực duy nhất của synteny bảo tồn được xác định thông qua việc nhóm BES của cá cầu vồng thành các contig dấu vân tay là 2,259, 2,229, và 2,203 cho stickleback, medaka, và cá đuối, tương ứng. Những con số này lớn gấp khoảng ba đến năm lần so với những gì chúng tôi đã xác định trước đó bằng cách sử dụng các đầu BAC. Phân nhóm kết quả phân tích synteny bảo tồn theo các nhóm liên kết như được phát deriv từ bản đồ tích hợp vật lý và di truyền cho thấy bất chấp sự đồng nhất trình tự thấp, có nhiều khối macrosynteny lớn được bảo tồn giữa các cánh nhiễm sắc thể của cá cầu vồng và các loài cá mô hình.

Từ khóa

#Cá cầu vồng #bộ gen #BAC #synteny #microsatellite

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