Concepedia

The libraries that made SUCEST

André L. Vettore, Felipe Rodrigues da Silva, Edson L. Kemper, Paulo Arruda

Genetics and Molecular Biology · 2001 · 244 citations · 14 references

Open access

Concepts

Life SciencesPlant BiologyPlant SciencesGenomicsPlant GenomicsPlant Molecular BiologyCrop GenomicsDna SequencingGene Library ConstructionGenome SequencingNucleic Acid SequencingPlant TranscriptomicsCdna CloningCdna Library ConstructionExpressed Sequence Tags Analysis

TL;DR

The study sequenced a large collection of sugarcane ESTs to begin mapping its genome. The authors constructed 26 unidirectional cDNA libraries from diverse tissues of 13 sugarcane cultivars, sequenced 291,689 clones at both ends, and estimated an average insert size of 1,250 bp. Filtering yielded 237,954 high‑quality ESTs that clustered into 43,141 groups, 38 % of which were novel, with 53 % represented in multiple libraries and 33 % containing full‑length inserts.

Abstract

A large-scale sequencing of sugarcane expressed sequence tags (ESTs) was carried out as a first step in depicting the genome of this important tropical crop. Twenty-six unidirectional cDNA libraries were constructed from a variety of tissues sampled from thirteen different sugarcane cultivars. A total of 291,689 cDNA clones were sequenced in their 5' and 3'end regions. After trimming low-quality sequences and removing vector and ribosomal RNA sequences, 237,954 ESTs potentially derived from protein-encoding messenger RNA (mRNA) remained. The average insert size in all libraries was estimated to be 1,250bp with the insert length varying from 500 to 5,000 bp. Clustering the 237,954 sugarcane ESTs resulted in 43,141clusters, from which 38% had no matches with existing sequences in the public databases. Around 53% of the clusters were formed by ESTs expressed in at least two libraries while 47% of the clusters are formed by ESTs expressed in only one library. A global analysis of the ESTs indicated that around 33% contain cDNA clones with full-length insert.