Abstract
BackgroundCotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence.Methodology/Principal FindingsIn this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves.Conclusions/SignificanceThese EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species.
Highlights
Cotton (Gossypium spp.) is the world’s most important agronomic fiber, as well as a significant oilseed crop
The results showed that the copies of these two genes decreased 145 and 200 fold, respectively, and suggested that the normalization quality of this library was good
In G. hirsutum, many expressed sequence tag (EST) are available, the total number is less than that of some field crops and model plants, and most ESTs in GenBank are from fibers or fiber-bearing ovules [11,32,33,34] and provide little or no information regarding leaf development
Summary
Cotton (Gossypium spp.) is the world’s most important agronomic fiber, as well as a significant oilseed crop. The seed is an important source of feed, foodstuff, and oil. The crop is widely cultivated in more than 80 countries, with China, India, the United States of America, and Pakistan the top four cotton producers China is the largest producer and consumer of raw cotton. Gossypium hirsutum L., or upland cotton, is a primary cultivated species and has an allotetraploid genome (AD; 2n = 4x = 52). Gossypium hirsutum produces over 90% of the world’s fibers because of its higher yield and wider environmental adaptability [1,2]. Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. Its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence
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