Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.
BACKGROUND
Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages.


RESULTS
Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories.


CONCLUSIONS
This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
Gorodkin
Jan
J
Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark. gorodkin@genome.ku.dk
Cirera
Susanna
S
Hedegaard
Jakob
J
Gilchrist
Michael J
MJ
Panitz
Frank
F
Jørgensen
Claus
C
Scheibye-Knudsen
Karsten
K
Arvin
Troels
T
Lumholdt
Steen
S
Sawera
Milena
M
Green
Trine
T
Nielsen
Bente J
BJ
Havgaard
Jakob H
JH
Rosenkilde
Carina
C
Wang
Jun
J
Li
Heng
H
Li
Ruiqiang
R
Liu
Bin
B
Hu
Songnian
S
Dong
Wei
W
Li
Wei
W
Yu
Jun
J
Wang
Jian
J
Staefeldt
Hans-Henrik
HH
Wernersson
Rasmus
R
Madsen
Lone B
LB
Thomsen
Bo
B
Hornshøj
Henrik
H
Bujie
Zhan
Z
Wang
Xuegang
X
Wang
Xuefei
X
Bolund
Lars
L
Brunak
Søren
S
Yang
Huanming
H
Bendixen
Christian
C
Fredholm
Merete
M
D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D020224:Expressed Sequence Tags; D015870:Gene Expression; D020869:Gene Expression Profiling; D015723:Gene Library; D023281:Genomics; D005810:Multigene Family; D012333:RNA, Messenger / Q000378:metabolism*; D013552:Swine / Q000235:genetics*
D012333:RNA, Messenger