Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus
© Osada et al; licensee BioMed Central Ltd. 2009
Received: 15 May 2009
Accepted: 29 September 2009
Published: 29 September 2009
Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. Macaca fascicularis is a macaque monkey that is commonly used for biomedical and ecological research.
We constructed cDNA libraries of Macaca fascicularis, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of Macaca fascicularis, which correspond to 56% of the curated human reference genes.
These sequences were deposited in the public sequence database as well as in-house macaque genome database http://genebank.nibio.go.jp/qfbase/. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.
Macaca fascicularis (cynomolgus, crab-eating, or long-tail macaque) is one of the most popular primate species used in biomedical research, and is closely related to Macaca mulatta (rhesus macaque). The draft sequence of the Macaca mulatta genome, which has an evolutionary important position, was published in 2007 .
Transcriptiome data broadens the application of genome sequences. Compared with several millions of human transcript sequences, macaque transcriptome data has only been analyzed in a limited numbers of studies [2–6]. A complete list of macaque genes will be beneficial for performing genetic studies using macaques in the future. We aim to elucidate all the macaque transcripts that correspond to human genes, which have been widely accepted as reference sequences, such as the RefSeq sequences .
We have published expressed sequence tag (EST) and full-length sequences, which were obtained from cDNA libraries of brain and testis of Macaca fascicularis, using a variety of research subjects [5, 8–13]. Here, we present 5'-EST sequences from six other tissues of Macaca fascicularis. Bone marrow, liver, pancreas, spleen, and thymus from a 4-year-old male Malaysian Macaca fascicularis, and kidney from a 3-year-old female Philippine Macaca fascicularis were harvested. These animals are bred and reared in the Tsukuba Primate Research Center (TPRC), National Institute of Biomedical Innovation (Ibaraki, Japan). The tissues were harvested in the P2 facility in TPRC, in accordance with the guidelines of the Laboratory Biosafety Manual, World Health Organization. The libraries for kidney (QreA and QreB) and liver (QlvC) were constructed using the vector-capping method , and those for bone marrow (QbmA), pancreas (QpaA), spleen (QspA), and thymus (QthA) were constructed using the oligo-capping method . The sequences of 5'-EST were determined by Sanger sequencing using an ABI 3730 sequencer, and all vector sequences were filtered out . Nucleotide calls with a quality value (QV) of less than 15 were masked as ambiguous. After the masking, the sequences were trimmed, such that they did not contain more than four ambiguous nucleotides in a 10-bp width window, and sequences shorter than 100 bp after the trimming were filtered out. After the trimming, the average sequence length was 886.9 bp.
In conjunction with the previously sequenced cDNA clones, we obtained 112,587 EST sequences corresponding to 8262 human RefSeq genes, which correspond to 36% of all human RefSeq genes. When we restricted the analysis of the human RefSeq genes in the manually curated status (Reviewed or Validated status) , 56% (6,177/11,080) of the human RefSeq genes were covered by the macaque transcriptome.
Summary of Macaca fascicularis cDNA libraries
Brain cortexa, c
Brain stemb, c
We have developed an in-house database for the genome data of Macaca fascicularis (QFbase: http://genebank.nibio.go.jp/qfbase/) . The Macaca fascicularis cDNA sequences described in this report were annotated and added to this database. They were also mapped on the rhesus macaque genome sequence using the BLAT program . The results can be viewed in the Macaca fascicularis genome browser http://genebank.nibio.go.jp/cgi-bin/gbrowse/rheMac2/, which is implemented using GBrowse software . The DDBJ/EMBL/Genbank accession numbers of these sequences are DC629777-DC639249 (bone marrow), DC639249-DC648806 (kidney), DC620589-DC629776 (liver), FS362802-FS372090 (pancreas), DC848487-DC858269 (spleen), and DK575154-DK584719 (thymus).
Availability and requirements
Project name: Macaca fascicularis cDNA sequencing project
Project home page: http://genebank.nibio.go.jp/qfbase/
Operating system(s): Platform independent
Programming language: PERL
Other requirements: Generic web browser
License: GNU, GPL
Any restrictions to use by non-academics: none
expressed sequence tag
This study was supported by a Health Science Research grant from the Ministry of Health, Labor, and Welfare of Japan.
- Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, et al: Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007, 316: 222-234. 10.1126/science.1139247.View ArticlePubMed
- Magness CL, Fellin PC, Thomas MJ, Korth MJ, Agy MB, Proll SC, Fitzgibbon M, Scherer CA, Miner DG, Katze MG, Iadonato SP: Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. Genome Biol. 2005, 6: R60-10.1186/gb-2005-6-7-r60.PubMed CentralView ArticlePubMed
- Chen WH, Wang XX, Lin W, He XW, Wu ZQ, Lin Y, Hu SN, Wang XN: Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system. BMC Genomics. 2006, 7: 82-10.1186/1471-2164-7-82.PubMed CentralView ArticlePubMed
- Wallace JC, Korth MJ, Paeper B, Proll SC, Thomas MJ, Magness CL, Iadonato SP, Nelson C, Katze MG: High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. BMC Genomics. 2007, 8: 28-10.1186/1471-2164-8-28.PubMed CentralView ArticlePubMed
- Osada N, Hashimoto K, Kameoka Y, Hirata M, Tanuma R, Uno Y, Inoue I, Hida M, Suzuki Y, Sugano S, et al: Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta. BMC Genomics. 2008, 9: 90-10.1186/1471-2164-9-90.PubMed CentralView ArticlePubMed
- Uno Y, Suzuki Y, Wakaguri H, Sakamoto Y, Sano H, Osada N, Hashimoto K, Sugano S, Inoue I: Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: a systematic identification of drug-metabolizing enzymes. FEBS Lett. 2008, 582: 351-358. 10.1016/j.febslet.2007.12.031.View ArticlePubMed
- Pruitt KD, Tatusova T, Klimke W, Maglott DR: NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009, 37: D32-36. 10.1093/nar/gkn721.PubMed CentralView ArticlePubMed
- Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K: Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain. Genome Biol. 2002, 3: RESEARCH0006-PubMed CentralPubMed
- Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Suto Y, Hirai M, Terao K, Sugano S, Hashimoto K: Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. BMC Genomics. 2002, 3: 36-10.1186/1471-2164-3-36.PubMed CentralView ArticlePubMed
- Osada N, Hida M, Kusuda J, Tanuma R, Iseki K, Hirata M, Suto Y, Hirai M, Terao K, Suzuki Y, et al: Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes. Gene. 2001, 275: 31-37. 10.1016/S0378-1119(01)00665-5.View ArticlePubMed
- Osada N, Hirata M, Tanuma R, Kusuda J, Hida M, Suzuki Y, Sugano S, Gojobori T, Shen CK, Wu CI, Hashimoto K: Substitution rate and structural divergence of 5'UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs. Mol Biol Evol. 2005, 22: 1976-1982. 10.1093/molbev/msi187.View ArticlePubMed
- Osada N, Kusuda J, Hirata M, Tanuma R, Hida M, Sugano S, Hirai M, Hashimoto K: Search for genes positively selected during primate evolution by 5'-end-sequence screening of cynomolgus monkey cDNAs. Genomics. 2002, 79: 657-662. 10.1006/geno.2002.6753.View ArticlePubMed
- Wang HY, Chien HC, Osada N, Hashimoto K, Sugano S, Gojobori T, Chou CK, Tsai SF, Wu CI, Shen CK: Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates. PLoS Biol. 2007, 5: e13-10.1371/journal.pbio.0050013.PubMed CentralView ArticlePubMed
- Kato S, Ohtoko K, Ohtake H, Kimura T: Vector-capping: a simple method for preparing a high-quality full-length cDNA library. DNA Res. 2005, 12: 53-62. 10.1093/dnares/12.1.53.View ArticlePubMed
- Maruyama K, Sugano S: Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene. 1994, 138: 171-174. 10.1016/0378-1119(94)90802-8.View ArticlePubMed
- Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110: 462-467. 10.1159/000084979.View ArticlePubMed
- Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2007, 35: D26-31. 10.1093/nar/gkl993.PubMed CentralView ArticlePubMed
- Chikaraishi DM, Deeb SS, Sueoka N: Sequence complexity of nuclear RNAs in adult rat tissues. Cell. 1978, 13: 111-120. 10.1016/0092-8674(78)90142-3.View ArticlePubMed
- Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664.PubMed CentralView ArticlePubMed
- Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res. 2002, 12: 1599-1610. 10.1101/gr.403602.PubMed CentralView ArticlePubMed
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