Isolation and annotation of 10828 putative full length cDNAs from indica rice

Kabin Xie, Jianwei - Zhang, Yong Xiang, Qi Feng, Bin Han, Zhaohui Chu, Shiping Wang, Qifa Zhang, Lizhong Xiong

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

Original languageEnglish (US)
Pages (from-to)445-451
Number of pages7
JournalScience in China, Series C: Life Sciences
Volume48
Issue number5
DOIs
StatePublished - 2005
Externally publishedYes

Fingerprint

genomics
rice
genome
Complementary DNA
homology
protein
open reading frames
proteins
proteomics
subspecies
cultivar
Genes
nucleotide sequences
gene
cultivars
Genome
Open Reading Frames
Oryza
genes
Databases

Keywords

  • Functional genomics
  • indica
  • Oryza sativa L.

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Isolation and annotation of 10828 putative full length cDNAs from indica rice. / Xie, Kabin; Zhang, Jianwei -; Xiang, Yong; Feng, Qi; Han, Bin; Chu, Zhaohui; Wang, Shiping; Zhang, Qifa; Xiong, Lizhong.

In: Science in China, Series C: Life Sciences, Vol. 48, No. 5, 2005, p. 445-451.

Research output: Contribution to journalArticle

Xie, K, Zhang, J, Xiang, Y, Feng, Q, Han, B, Chu, Z, Wang, S, Zhang, Q & Xiong, L 2005, 'Isolation and annotation of 10828 putative full length cDNAs from indica rice', Science in China, Series C: Life Sciences, vol. 48, no. 5, pp. 445-451. https://doi.org/10.1360/062004-90
Xie, Kabin ; Zhang, Jianwei - ; Xiang, Yong ; Feng, Qi ; Han, Bin ; Chu, Zhaohui ; Wang, Shiping ; Zhang, Qifa ; Xiong, Lizhong. / Isolation and annotation of 10828 putative full length cDNAs from indica rice. In: Science in China, Series C: Life Sciences. 2005 ; Vol. 48, No. 5. pp. 445-451.
@article{a21edce158914aa3bdfe5c9c205088a8,
title = "Isolation and annotation of 10828 putative full length cDNAs from indica rice",
abstract = "We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53{\%} of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28{\%}) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78{\%}) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2{\%}. A majority of FL-cDNAs (90{\%}) could be classified with GO (gene ontology) terms based on homology proteins. More than 60{\%} of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.",
keywords = "Functional genomics, indica, Oryza sativa L.",
author = "Kabin Xie and Zhang, {Jianwei -} and Yong Xiang and Qi Feng and Bin Han and Zhaohui Chu and Shiping Wang and Qifa Zhang and Lizhong Xiong",
year = "2005",
doi = "10.1360/062004-90",
language = "English (US)",
volume = "48",
pages = "445--451",
journal = "Science in China, Series C: Life Sciences",
issn = "1006-9305",
publisher = "Science in China Press",
number = "5",

}

TY - JOUR

T1 - Isolation and annotation of 10828 putative full length cDNAs from indica rice

AU - Xie, Kabin

AU - Zhang, Jianwei -

AU - Xiang, Yong

AU - Feng, Qi

AU - Han, Bin

AU - Chu, Zhaohui

AU - Wang, Shiping

AU - Zhang, Qifa

AU - Xiong, Lizhong

PY - 2005

Y1 - 2005

N2 - We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

AB - We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5′UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

KW - Functional genomics

KW - indica

KW - Oryza sativa L.

UR - http://www.scopus.com/inward/record.url?scp=33749862210&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33749862210&partnerID=8YFLogxK

U2 - 10.1360/062004-90

DO - 10.1360/062004-90

M3 - Article

C2 - 16315595

AN - SCOPUS:33749862210

VL - 48

SP - 445

EP - 451

JO - Science in China, Series C: Life Sciences

JF - Science in China, Series C: Life Sciences

SN - 1006-9305

IS - 5

ER -