Location: Genomics and Bioinformatics Research2012 Annual Report
1a. Objectives (from AD-416):
In order to facilitate the sequencing and assembly of the genome of cultivated cotton, DNA sequences are needed that will act as long scaffolding of the assembly process. Ideally some of these would be generated from ends of DNA fragments that range from 100,000 bp to 160,000 bp. This project will generate Bacterial Artificial Chromosome (BAC) end sequene flow 40,000 to 50,000 BACs.
1b. Approach (from AD-416):
The DNA segments are to be cloned into a Bacterial Artificial Chromosome (BAC) vector. The BAC libraries are being made by Clemson University Genomics Institute in conjunction with an ongoing National Science Foundation (NSF) project on cotton fiber. DNA sequences will be generated from each end of the DNA fragment and will be recorded as pairs to allow for genome assembly software to use them as paired end reads. The DNA source will be Tm-1 which is a variety of scientific importance to the cotton research community. Clemson University will be producing DNA fingerprints from the BACS and that DNA will be used to generate BAC end DNA sequence of 40,000 BACs. The data will be released following standard ARS policies in regard to DNA sequence information.
3. Progress Report:
The goal of this project is to develop genomics resources for the eventual sequencing of the cotton genome. In a related National Science Foundation, 100,000 Bacterial Artificial Chromosomes (BACs) containing the cotton genome in large fragments are being DNA fingerprinted to create a physical map. To help associate the BACs to the known cotton genetic map and help in the assembly of the cotton genome the ends of these BACs are being sequenced. To date ~100,000 BAC end sequences have been generated with ~90% success rate. Participants converse through mainly emails, quarterly reports, face to face meetings or phone conversations.