Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle.
An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high-throughput sequencing. The libraries were made with RNA pooled from multiple tissues to increase efficiency of normalization and maximize the number of independent genes for which sequence data were obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter- and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed in combination with 56,500 other bovine EST sequences present in the GenBank dbEST database to construct a cattle Gene Index (available from The Institute for Genomic Research at http://www.tigr.org/tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the Web site. Analysis of individual library sequence data indicates that the pooled-tissue approach was highly effective in preparing libraries for efficient deep sequencing.
Smith
T P
TP
United States Department of Agriculture, Agricultural Research Service, United States Meat Animal Research Center, Clay Center, Nebraska 68933, USA. smith@email.marc.usda.gov
Grosse
W M
WM
Freking
B A
BA
Roberts
A J
AJ
Stone
R T
RT
Casas
E
E
Wray
J E
JE
White
J
J
Cho
J
J
Fahrenkrug
S C
SC
Bennett
G L
GL
Heaton
M P
MP
Laegreid
W W
WW
Rohrer
G A
GA
Chitko-McKown
C G
CG
Pertea
G
G
Holt
I
I
Karamycheva
S
S
Liang
F
F
Quackenbush
J
J
Keele
J W
JW
D000818:Animals; D002417:Cattle; D016208:Databases, Factual; D020224:Expressed Sequence Tags; D005260:Female; D005333:Fetus; D020869:Gene Expression Profiling / Q000379:methods; D015723:Gene Library; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009928:Organ Specificity / Q000235:genetics; D011247:Pregnancy