Abstract
BackgroundWith the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.ResultsHere we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.ConclusionAnalysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.
Highlights
With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants
Comparison of bamboo cDNAs and rice genes involved in lignin biosynthesis suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as effective targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping
The average length of these FL-cDNAs was 1,092 bp, and 8,695 (82%) cDNAs had open reading frames (ORFs) longer than 100 amino acids, similar to 87% in soybean [10] and 91% in poplar [11]. The characteristics of these 8,695 cDNAs were compared with 37,165 FL-cDNAs of rice and 17,390 FLcDNAs of Arabidopsis with predicted ORFs longer than 100 amino acids
Summary
With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. With the number of genome sequences growing much more rapidly than any other plant family, the grass family (Poaceae) becomes an ideal system for comparative studies of gene and genome structure and function [1,2,3,4,5,6]. It is critical to accumulate genomic resources for all major lineages of the grass family. More serious than the missing link for comparative analyses is the lack of genomic resources of bamboo This hampers biological investigations of this group of morphologically and physiologically unique and ecologically and economically important grasses. In addition to remarkable sizes and woodiness, bamboo has rather striking life history characterized by a prolonged vegetative phase lasting up to more than 100 years before flowering
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