Large-scale sequencing of plant genomes

Current Opinion in Plant Biology

Volumn 1, Issue 2, 1998, Pages 136-141

  Rounsley, Steve ^a   Lin, Xiaoying ^a   Ketchum, Karen A ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENOME; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; SEQUENCE ANALYSIS, DNA;

EID: 0032034740     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(98)80015-0     Document Type: Article

References (13)

1. Adams M, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF et al.: Complementary DNA sequencing: expressed sequence tags and human genome project Science 1991, 252:1651-1656.
2. Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M et al.: Genes galore: a summary of the methods for accessing the results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 1994, 106:1241-1255.
3. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D et al.: An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 1993, 4:1051-1061.
4. Yamamoto K, Sasaki T: Large-scale EST sequencing in rice. Plant Mol Biol 1997, 35:135-144. Summarizes the progress to date in the rice EST sequencing program in Japan.
5. Cohen J: Please pass the data. Science 1997, 276:1961.
6. Boguski MS, Lowe TMJ, Tolstoshev CM: dbEST-database for 'expressed sequence tags'. Nat Genet 1993, 4:332-333.
7. dbEST on World Wide Web URL: http://www.ncbi.nlm.nih.gov/dbEST/index.html This web site is the central repository for EST sequences from all species. Each EST is regularly searched against the nucleotide and protein databases and similarity results are stored. Sequence data is also searchable through the BLAST server.
8. Plant Molecular Informatics Center on World Wide Web URL: http://www.cbc.med.umn.edu /ResearchProjects/seq.proc.html
9. Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC, Kerlavage AR: The construction of Arabidopsis expressed sequence tag assemblies. Plant Physiol 1996, 112:1177-1183. The process of assembling ESTs into contigs is described and this paper also contains some estimates for a number of genes represented by the EST collection.
10. Cooke R, Raynal M, Laudié M, Delseny M: Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J 1997, 11:1127-1140. Describes a similar approach of assembling ESTs as in [9*] but restricted to the ribosomal proteins.
11. Rice Gene Index on World Wide Web URL: http://www.tigr.org/tdb/ogi/
12. Arabidopsis EST Assemblies on World Wide Web URL: http://www.tigr.org/tdb/at/at.html
13. Tremousaygue D, Bardet M, Dabos P, Regad F, Pelese F, Nazer R, Gander E, Lescure B: Genome DNA sequencing around the EF-1α multigenic locus of Arabidopsis thaliana indicates a high gene density and a shuffling of non-coding regions. Genome Res 1997, 7:198-209.