Genes Galore: A Summary of Methods for Accessing Results from Large-Scale Partial Sequencing of Anonymous Arabidopsis cDNA Clones

Abstract

94305-41 O1 (S.S., C.S.)High-throughput automated partial sequencing of anonymous cDNA clones provides a method to survey the repertoire of expressed genes from an organism. Comparison of the coding capacity of these expressed sequence tags (ESTs) with the sequences in the public data bases results in assignment of putative fundion to a significant proportion of the ESTs. Thus, the more than 13,400 plant ESTs that are currently available provide a new resource that will facilitate progress in many areas of plant biology. These opportunities are illustrated by a description of the results obtained from analysis of 1500 Arabidopsis ESTs from a cDNA library prepared from equal portions of poly(A+) mRNA from etiolated seedlings, roots, leaves, and flowering inflorescences. More than 900 different sequences were represented, 32% of which showed significant nucleotide or deduced amino acid sequence similarity to previously charaderized genes or proteins from a wide range of organisms. At least 165 of the clones had significant deduced amino acid sequence homology to proteins or gene products that have not been previously characterized from higher plants. A summary of methods for accessing the information and materials generated by the Arabidopsis cDNA sequencing projeds is provided.

Molecular and structural analyses of a novel temperature stress‐induced lipocalin from wheat and Arabidopsis

“…The 28S ribosomal band stained with ethidium bromide is included to show RNA loads (7.5 Wg). NA7, NA12, non-acclimated plants grown for 7 and 12 days; CA1, CA6, CA36, cold-acclimated plants for 1,6 and 36 days; DA1 and DA5, coldacclimated plants (36 days) were deacclimated for 1 and 5 days; NaCl, plants treated with 300 mM NaCl for 18 h; ABA, plants treated with 0.1 mM ABA (Sigma) for 18 h; WS, water-stressed plants with a relative water content of 57% and 44%; HS, plants exposed to 40 ‡C for 1 h and 3 h (heat-shock); W, wounding stress for 3 h. Leaf, crown and roots of non-acclimated plants (NA7) and 6 days cold-acclimated (CA6). ARA, Arabidopsis plants; NA, nonacclimated plants; CA1, cold-acclimated for 1 day; HS 1 h, exposed to 45 ‡C for 1 h (heat-shock).…”

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

“…Only comparisons that resulted in BLAST scores >80, indicating significant sequence similarity, are discussed (Newman et aL, 1994).…”

Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins

“…This length was chosen as it is the average length of sequences submitted to EMBL by the European sequencing consortium (Cooke et aL, 1996;H6fte et aL, 1993) and thus corresponds to the average length of high-quality sequence data which can be obtained from a singlepass sequencing run. These trimming criteria were applied to all sequences from the American project (Newman et aL, 1994). Longer, manually corrected sequences from the European consortium were left unedited if they contained no ambiguities.…”