- Research article
- Open Access
A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation
© Bonnet et al; licensee BioMed Central Ltd. 2008
- Received: 23 August 2007
- Accepted: 14 January 2008
- Published: 14 January 2008
Domestic animal breeding and product quality improvement require the control of reproduction, nutrition, health and welfare in these animals. It is thus necessary to improve our knowledge of the major physiological functions and their interactions. This would be greatly enhanced by the availability of expressed gene sequences in the databases and by cDNA arrays allowing the transcriptome analysis of any function.
The objective within the AGENAE French program was to initiate a high-throughput cDNA sequencing program of a 38-tissue normalised library and generate a diverse microarray for transcriptome analysis in pig species.
We constructed a multi-tissue cDNA library, which was normalised and subtracted to reduce the redundancy of the clones. Expressed Sequence Tags were produced and 24449 high-quality sequences were released in EMBL database. The assembly of all the public ESTs (available through SIGENAE website) resulted in 40786 contigs and 54653 singletons. At least one Agenae sequence is present in 11969 contigs (12.5%) and in 9291 of the deeper-than-one-contigs (22.8%). Sequence analysis showed that both normalisation and subtraction processes were successful and that the initial tissue complexity was maintained in the final libraries. A 9K nylon cDNA microarray was produced and is available through CRB-GADIE. It will allow high sensitivity transcriptome analyses in pigs.
In the present work, a pig multi-tissue cDNA library was constructed and a 9K cDNA microarray designed. It contributes to the Expressed Sequence Tags pig data, and offers a valuable tool for transcriptome analysis.
- External Control
- Gene Ontology Annotation
- Subtraction Process
- PolyA Site
- Normalise Library
In pigs, like in other domestic animals, breeding and product quality improvement require the control of several different traits (reproduction, nutrition, health and welfare). It is thus necessary to improve our knowledge of the major physiological functions and their interactions. For this purpose, the French National Institute for Agricultural Research (INRA)  has launched a genomic research program, AGENAE (Analyse du GENome des Animaux d'Elevage)  for the identification and the functional and genetic characterisation of a large number of genes in cattle, pigs, chicken and trout .
With the shift from map-based towards sequence-based gene discovery, the prevailing approach for creating transcription maps has become the generation of Expressed Sequence Tags . In pigs, the first EST project  and first large-scale EST project were reported  about ten years ago. Subsequently, several research groups have generated ESTs from cDNA libraries constructed from either a single porcine tissue or a limited number of tissues related to a stage of development or a function, such as anterior pituitary [7, 8], backfat , brain , liver , skeletal muscle [12–14], immune system tissues , reproductive tissues [8, 16, 17] and embryo [17–19]. The construction of full-length cDNA libraries was reported more recently [20–22].
To date, the construction of several pig arrays have been reported. Some of them, with various supports, contain 1 to 4000 cDNA from specific libraries: brain tissue (GEO database accession number GPL336), muscle  (GPL518) (GPL2731), embryo  (GPL1209), immune system cells [26, 27] (GPL1624), but others aim at a generic analysis (10 to 20000 genes) of pig transcriptome with glass slides of in situ-synthesised oligonucleotides (Affymetrix, GPL3533), spotted oligonucleotides (Operon-Qiagen set) (GPL 1881, GPL3461, GPL3707) or cDNAs (GPL3585, GPL3608).
We report here the construction of a pig multi-tissue cDNA library, its sequencing and analysis, and the generation of a 9K nylon micro-array public tool for large scale expression profiling experiments.
cDNA libraries construction and characterisation
Description of the different libraries
Adult (A), young (Y) or fetal (F) animal
Number of recombinant clones
Pituitary gland (A)
Cerebral trunk (A)
Stomach (A + F)
Small intestine (A + F)
Large intestine (A + F)
Liver (A + F)
Thymus (A + Y)
4-Heart and muscle
Heart (A + F)
1 800 000
Muscle (A + F)
Adipose tissue (A)
5-Male reproductive organs
Seminal vesicle (A)
Bulbourethral gland (A)
6-Female reproductive organs
1 325 000
Ovary (A + F)
Mammary gland (A)
Mix of libraries 1 to 6
6 400 000
After a first round of sequencing, the library was subtracted with the 8736 already-sequenced clones. The subtracted library contained 60 000 clones. The quality of the subtraction was assessed by the sequencing of 384 clones (see below).
Number of sequenced and released ESTs from the two Agenae libraries
Number of sequenced clones
Number of 5' sequences
Number of 3' sequences
Number of sequences
In the first 384-sequences from the subtracted library, the proportion of 28S RNA sequences had decreased towards 0.52% and 95.1% sequences were new, in comparison with the normalised library. The proportion of empty clones was still about 2%. A total of 14976 clones were then 5'-end sequenced and 12778 (85.3%) sequences were released in the EMBL-EBI nucleotide database (Table 2) . Sequencing was then stopped: the redundancy had reached 39% (Figure 2). The EMBL accession numbers are listed in supplemental data 1. PolyA was detected in 41.5% of the sequences. Polyadenylation signal was detected in 52.9% of the polyA-containing sequences. The sequence of the medium-frequency external control (luciferase) was present 5 times. The other two external control sequences were still not detected.
The library construction method (through the excess of oligo(dT) during the first reverse transcription) led to short polyA 3'-end stretches, allowing almost the same validity rate of the sequences either from 5' (82.2%) or 3' (80.9%)-end. Thus, even if 3'-end sequencing is useful to distinguish genes in a closely related family as the 3'-end non coding regions are more divergent, the 5'-end sequencing strategy was favoured to provide better annotated clones.
Sequence assembly and analysis
Agenae contribution to public sequence data
The number of contigs highly depends on the parameters used when assembling the sequences. The TIGR pig clustering, with nearly the same amount of data, lead to 64,746 contigs and 88,274 singletons. Careful annotation of the contigs and the next completion of the pig genome sequence may show that paralogous genes are sometimes clustered and that, on the contrary, overlapping contigs may have been split up. UniGene clustering  lead to 32,711 contigs and 7,230 singletons. The low number of singletons in UniGene assembly is probably due to the fact UniGene does not use part of the available singletons, as was already noticed with trout data .
Quality of the libraries
20 deepest contigs
Best swissprot hit
Best SP hit accession
Best SP hit description
Best SP hit evalue
Tubulin alpha-ubiquitous chain (Alpha-tubulin ubiquitous) (Tubulin K-alpha-1)
Elongation factor 1-alpha 1 (EF-1-alpha-1)
ADP/ATP translocase 3 (Adenine nucleotide translocator 2) (ANT 3)
Alpha-1-antichymotrypsin precursor (ACT)
Vitronectin precursor (Serum spreading factor) (S-protein)
Ferritin light chain (Ferritin L subunit)
Guanine nucleotide-binding protein beta subunit 2-like 1
Translationally-controlled tumor protein (TCTP)
40S ribosomal protein S21
60S acidic ribosomal protein P0 (L10E)
Ferritin heavy chain (EC 220.127.116.11) (Ferritin H subunit)
Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)
Hemoglobin alpha subunit (Hemoglobin alpha chain) (Alpha-globin)
Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]
Serum albumin precursor
Cytochrome P450 2D25 (EC 1.14.14.-) (CYPIID25) (Vitamin D(3) 25-hydroxylase)
Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma) (Fragment)
Dehydrogenase/reductase SDR family member 4 (EC 18.104.22.168)
60S ribosomal protein L3
HLA class II histocompatibility antigen, DR alpha chain precursor
The analysis of the sequences obtained from the normalised library revealed a contamination by 28S ribosomal RNA This type of contamination has already been described in cDNA libraries . This sequence has been over-represented in the subtraction driver and the analysis of the sequences from the subtracted library reveals the presence of 127 out of 14,976 28S ribosomal clones (0.85%). The proportion of this contamination has then been reduced by about 5.
20 deepest Agenae specific contigs
Best swissprot hit
Best SP hit accession
Best SP hit description
Best SP hit e-value
Chymotrypsinogen 2 precursor (EC 22.214.171.124)
Prostatic spermine-binding protein precursor (SBP)
Forkhead box protein K2 (Interleukin enhancer-binding factor 1)
Anionic trypsin precursor (EC 126.96.36.199)
PDZ domain-containing protein 4
Nuclear receptor corepressor 1 (N-CoR1) (N-CoR)
Zinc finger and BTB domain-containing protein 4
Bile-salt-activated lipase precursor (EC 188.8.131.52)
BTB and kelch domain containing protein 5
Host cell factor (HCF) (HCF-1) (C1 factor) (VP16 accessory protein)
Creatine kinase, sarcomeric mitochondrial precursor (EC 184.108.40.206)
Adiponutrin (iPLA2-epsilon) [Includes: Triacylglycerol lipase (EC 220.127.116.11)
Oligodendrocyte transcription factor 2 (Oligo2) (Basic helix-loop-helix protein class B 1)
Nuclear receptor corepressor 1 (N-CoR1) (N-CoR)
Beta-defensin 109 precursor (Defensin, beta 109)
Best swissprot hit
Genbank accession number
Sigenae contig name
Microarray design and production
Among the 95439 SIGENAE pig contigs, 8931 different contigs were chosen. For 7749 of them, at least one representing clone belonged to the multi-tissue library and had an insert size compatible with PCR amplification (data not shown). Other contigs were either represented by a USDA clone (835)  or a subtractive suppression library clone (188) (Agnès Bonnet, personal communication). Other clones come from different home-made libraries (159) and 285 controls were also included (78 empty controls, 12 empty-vector controls and 195 spikes).
Microarray quality control
This nylon array is a valuable tool for transcriptome analysis. The use of radiolabelled complex probes allows to detect low-expressed mRNAs using small total RNA amounts (about 100 ng of total RNA) . Such arrays have been used in several studies on human cancer  trout reproduction  and pig transcriptome , Rigaldie, E and Liaubet, L personal communications).
Microarray Gene Ontology
We constructed a pig multi-tissue cDNA library which has been successfully normalised and subtracted. This library is derived from the most diverse tissue representation to date. It provides a large set of clones, with limited redundancy but good representation of the complex set of initial tissues. The 24,449 sequences allowed a precise characterisation of the library and contributed to international cDNA sequencing effort.
The 9K nylon cDNA microarray is now used in several gene expression profiling projects, in pig health, reproduction and meat quality.
Tissue collection and RNA preparation
Research involving animal experimentation is approved and controlled by INRA (Institut National de la Recherche Agronomique) (authorisation B-35-275-32 and A37801). Animals were either reared at UE967 Génétique expérimentale en productions animales in Le Magneraud (France) and slaughtered at the Unité Mixte de Recherche SENAH in Saint Gilles (France) or reared and slaughtered at Unité Pluri-Espèces d'Expérimentation Animale in Tours-Nouzilly (France). Forty-four tissue samples from Meishan and Large White pigs at different stages of development or in different physiological conditions (foetus, young or adult animal, male or female, pregnant, stressed or control animals) were taken, frozen in liquid nitrogen and stored at -80°C until RNA extraction.
Total RNA was extracted, using the Chomczynski method  and controlled (integrity, reverse transcription efficiency) resulting in 38 high quality preparations.
These total RNA were pooled into 6 groups in equal proportions, according to biological functions (Table 1): brain, digestive function, glands, heart and muscle, male reproduction, female reproduction. PolyA+ mRNA was extracted from 300 μg of RNA from these pools.
As a control, 3 exogenous polyA+ mRNAs ("spikes") obtained by in vitro transcription of the corresponding cDNA sequences of SRG3 (A. thaliana, X98376), luciferase (P. pyralis, CVU03687) and I11a (A. thaliana, Y10291) were added to the polyA+ RNAs of each library in different amounts: 6.578 ng, 104.15 pg and 0.274 pg/μg pig RNA respectively. These concentrations correspond to the respective estimated frequencies of 0.5, 50 and 5000 copies of mRNA per cell.
Library construction, normalisation and subtraction
The libraries were constructed, normalised and subtracted following the protocol of Soares  with minor modifications. Briefly, 1 μg of polyA+ RNA (including the 3 spikes) from each pool was used and the reverse transcription with Superscript II (Invitrogen) was primed with 1 μg of NotI-Tag-dT18 primer (see Additional file 2), containing the sequence AGCAG as a library tag. Second-strand synthesis was performed with T4 DNA polymerase (Biolabs) in the presence of DNA ligase (Biolabs) and RNase H (Amersham Pharmacia biotech). cDNA were size-selected (>500 bp), using a BioGel A 50 (BioRad) gel filtration, ligated to EcoRI adaptators primer (see Additional file 2) (Amersham Pharmacia biotech) and digested with NotI. The purified cDNAs were directionally cloned into a pT3T7-pac vector and electroporated into DH10B E coli bacteria. The number of recombinant clones was determined, for each library, by dilution titration of bacteria onto ampicillin plates. The whole six libraries were pooled and the resulting library was normalised.
The normalisation was achieved through the reassociation of an excess of cDNA inserts, amplified by PCR, with single-stranded plasmid circles, obtained from the starting library (I) . Single-stranded plasmids were generated in vivo and purified by chromatography on hydroxyapptite (HAP). One ng of the single-stranded library was used in a high-fidelity PCR (Qiagen Taq Polymerase, 250 UI, reference 201203) with T3 and T7 primers primer (see Additional file 2). 500 ng of PCR products were mixed with 50 ng of the single-stranded library and allowed to hybridise for 22 hours (Cot = 5). The remaining single-stranded circles were purified by HAP chromatography, converted into double-stranded plasmids with T7 sequenase (USB, reference 707752), and electroporated into DH10B bacteria. This led to the normalised library (N) The bound double-stranded fraction was recovered from the HAP column and used to generate a mini-library (A) enriched for abundant mRNAs.
The rate of empty clones and the average size of the inserts were estimated by a PCR amplification of the inserts from 96 clones, by using primers (M13/24 and M13Raster, see Additional file 2) flanking the vector-cloning sites primer.
The subtraction was achieved in a similar way using a Cot = 50: 50 ng of the single-stranded normalised library was reassociated with 2.5 μg of PCR products (primers M13/24 and M13Raster, see Additional file 2) generated from the 8736 sequenced clones of the normalised library. In order to eliminate one over-represented contig, 10% of these PCR products were generated from 4 clones chosen to represent the consensus sequence of this contig.
The quality of the normalisation or subtraction was assessed using the external controls in southern blot and PCR experiments. For southern blot experiment, 500 ng of the I, A and N libraries were separated by electrophoresis on a 1% agarose gel and blotted onto a nylon membrane. The blot was hybridised with a labelled probe corresponding to the external controls. PCR experiments were done with specific primers for external controls (see Additional file 2): 30 cycles of amplification were performed, using different amounts of plasmid DNA from each library (A, I or N) as a template. The PCR products were analysed on 1% agarose gel. The sequencing of 96 to 384 randomly picked clones was also used to assess the quality of the normalisation or subtraction processes.
The recombinant bacteria were plated onto 2YT/ampicillin plates and picked into 96 or 384-well plates using a BioPick (Génopole de Toulouse) or a QPix (CRB-GADIE ) robot and grown in 10% glycerol medium. Four copies of the plates were made and stored at -80°C. Control plates were generated by picking 2 or 8 (96 or 384-well plates) clones from each sequencing plate. They were also sequenced and used as a sequence-quality control.
A total of 23712 clones were sequenced, following plasmid DNA preparation, from either 5' or both ends by MilleGen® Biotechnologies  using M13 (-43) or M13R (-47) primers (see Additional file 2) andBigDye V3.1 (Applied Biosystem) or ET terminator (Amersham) chemistries.
Sequence analysis and clustering
The data files produced by MilleGen® Biotechnologies were processed by SIGENAE and the documentation on the procedures is available on SIGENAE website . Briefly, the sequences were cleaned up from vector and adaptator sequences; repeats and contaminants were removed by comparison with several sequence databases: Univec, Yeast and E. coli genomes as well as pig ribosomal and mitochondrial genomes. Exogenous control sequences were also removed. PolyA site was identified by its relative position to the vector multiple cloning site and 2 putative polyadenylation sites (AATAAA or ATTAAA) were searched within the 30 bases preceding the polyA site. Valid sequences, that is with a PHRED score over 20 on at least 100 bp, were submitted to the EMBL-EBI Nucleotide Sequence database . All public pig sequences were clustered. Redundancy of the library was calculated as follows: redundancy = 1 - (number of genes/number of clones). The number of genes is estimated by the number of contigs obtained at the end of the SIGENAE processing chain.
The identification and annotation retrieval of the 20 deepest contigs of the assembly and of the 20 deepest AGENAE specific contigs was done by SQL requests on the SIGENAE database. For the deepest contigs, the sequences from Agenae libraries were counted.
Sequences corresponding to putative "tissue specific" proteins in the normalised or subtracted library were identified using a best blast hit strategy for the approximation of ortholog pig genes. The tissue-specificity was documented by literature and the contig containing the nucleotide sequence of the gene referenced in the publication was searched through the SIGENAE WEB interface. If the publication of the sequence was posterior to the SIGENAE assembly, a blastn of the sequence against public_pig_contigV3 database was performed and the contig with a 0 E-value considered. Then an AGENAE sequence was identified in the contig.
Microarray design, production, quality control and Gene Ontology analysis
According to clone availability, the contigs represented by at least one Agenae or USDA clone were selected and the size of the insert was estimated for the different clones.
The following descending order criteria were examined:
the size of the insert had to be between 0.7 and 1.5 kb-long
priority was given to a Agenae clone
priority was given to the longest-insert Agenae clone
Other clones came from home-made libraries and chosen by INRA researchers.
The 9138 selected clones have been rearrayed from different libraries. The origin plates were replicated in 384 wells plates in a fresh version for a best result of the subsequent rearraying. These steps were conducted using a Q-Bot robot (Genetix, UK). The bacteria were grown overnight in 2YT (Yeast Tryptone) culture medium containing carbenicilin (100 μg/ml) and glycerol (8%).
To assess the quality of the different steps from sequencing to rearraying, the 4 corners of all plates were controlled by sequencing (4 clones/corner); the obtained sequences were compared with the expected sequences.
PCR amplifications were performed in 96-well microtiter plates using the u-pig-CRB and l-pig-CRB primers (see Additional file 2), which were specific of the polylinker sequence of vectors used (pCMVSPORT6 for USDA libraries and pT7T3D-pac, pbluescript, pCR 2.1-topo, pUC for INRA libraries). The reactions were performed by transferring 4 μl of Escherichia coli in growth culture to 100 μl of PCR mix, containing 1.5 mM MgCl2, 1 M betaine, 100 μM dATP, dTTP, dGTP, and dCTP, 1× Promega buffer and 5 U of Taq polymerase (M1865, Promega, Madison, WI). All the steps were conducted by a RapidPlate liquid-handling machine (Caliper LifeSciences). The plates were incubated for 3 min at 94°C, before 35 cycles of 94°C for 30 s, 60°C for 30 s and 72°C for 120 s. Amplification products were not quantified, but their quality was systematically checked on 1% agarose gels.
unpurified PCR products were evaporated, resuspended in 20 μl of distilled water, then transferred to 384-well microplates and spotted ontonylon membranes (Hybond-N+; Amersham Biosciences, Saclay, France), using a Biorobotics MicroGrid-II arrayer (Genomics Solution, Cambridge, U.K.) equipped with a 64-pins Bioroboticsprinthead and 64 Biorobotics 100 μm solid pins. The spotted DNA was denaturated in 150 mM NaOH, 1.5 M NaCl, neutralised in 1 M Tris HCl (pH 7.5), 1.5 M NaCl. After rinsing micromembranes in 2× SSC, the DNA was fixed by successive heat (80°C during 2 hours) and UV (120000 μJ) treatments.
to control the quality of the nylon microarrays, a vector probe hybridisation (5'-TCACACAGGAAACAGCTATGAC-3')was performed (as described in http://tagc.univ-mrs.fr/pub/Cancer/) on 8% of the micromembranes.
Gene Ontology analysis
The consensus sequence of all the contigs were blasted (blastx, e-value < 10-5) against SwissProt database (version 48). The Gene Ontology annotations were recovered from the best swissprot hit. The proportion of annotated contigs and the proportion of each GO term category was calculated for 2 data sets: 9K microarray contigs and all SIGENAE contigs. A chi-square test (p-value < 0.001) was performed to test if the microarray was enriched in particular GO terms.
We thank the colleagues who provided the different pig tissues and/or RNA extracts. We thank Laurent Mazzolini and Véronique Duranthon for providing external controls. We thank Philippe Mulsant for his help during Gwenola Tosser-Klopp's maternity leave, Sandrine Villeger and Cédric Cabau for technical help. We are grateful to Béatrice Loriod and her colleagues from CIML for their help with microarray spotting technique. This work was part of the French National program AGENAE.
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