Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jun 18:10:116.
doi: 10.1186/1471-2229-10-116.

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

Zhenhua Peng  1 , Tingting Lu, Lubin Li, Xiaohui Liu, Zhimin Gao, Tao Hu, Xuewen Yang, Qi Feng, Jianping Guan, Qijun Weng, Danlin Fan, Chuanrang Zhu, Ying Lu, Bin Han, Zehui Jiang
Affiliations

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

Zhenhua Peng et al. BMC Plant Biol. .

Abstract

Background: 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.

Results: Here 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.

Conclusion: Analysis 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Types and frequency of occurrence of simple sequence repeats (SSRs) in cDNAs of bamboo, rice, and Arabidopsis. (A) Percentage of SSRs in different period sizes. Relative abundance of different types of SSRs is classified according to repeat length. (B) Frequency of SSR sequences in different types. Relative frequency of 14 most abundant repeat sequences of SSRs is shown. (C) Frequency and position of mono-, di-, and tri-nucleotide SSRs. Frequency distribution of mono-, di-, and tri-nucleotide SSRs are calculated along the predicted transcribed regions.
Figure 2
Figure 2
Phylogeny of grasses inferred from concatenated alignment of 43 putative orthologous cDNA sequences. (A) Tree inferred from maximal likelihood method. Bayes inference yielded the same topology. (B) Tree inferred from neighbor joining method. Branch length is proportional to estimated sequence divergence measured by scale bars. Numbers associated with branches are bootstrap percentages. Arabidopsis was used as outgroup. Subfamily affiliation of the grasses is indicated at right.
Figure 3
Figure 3
Bamboo cDNA similarity comparison and functional classification. (A) Similarity search of bamboo sequence against closely related grasses. Right half of the pie, the proportion of bamboo cDNAs with homologs in rice, of which the proportion that also hit barley, wheat, and Brachypodium is colored blue. Left half, bamboo cDNAs with no homologs found in rice, of which the proportion that also had no hit in the barley, wheat, and Brachypodium is colored gray. (B) Functional classification of bamboo cDNAs with and without homologs with other grasses. Blue bars represent cDNAs from the blue portion of the pie shared by all grasses compared, and gray bars represent cDNAs from the gray portion of the pie which is presumably bamboo unique.
Figure 4
Figure 4
Distribution and functional classification of bamboo cDNAs according to sequence divergence compared with rice cDNAs. Red curve shows distribution of bamboo cDNAs according to synonymous divergence (KS) with rice homologs. Dots, corresponding nonsynonymous divergence (KA). Only cDNAs with KS < 0.75 are shown.
Figure 5
Figure 5
Distribution of divergence time. X axis is the divergence time (mya) of homologous pairs, Y axis is the number of detected EST clusters.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Gale MD, Devos KM. Comparative genetics in the grasses. Proc Natl Acad Sci USA. 1998;95:1971–1974. doi: 10.1073/pnas.95.5.1971. - DOI - PMC - PubMed
    1. Gaut BS. Evolutionary dynamics of grass genomes. New Phytologist. 2001;154:15–28. doi: 10.1046/j.1469-8137.2002.00352.x. - DOI
    1. Bennetzen JL. Patterns in grass genome evolution. Curr Opin in Plant Biol. 2007;10:176–181. doi: 10.1016/j.pbi.2007.01.010. - DOI - PubMed
    1. Buell CR. Poaceae genomes: Going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiol. 2009;149:111–116. doi: 10.1104/pp.108.128926. - DOI - PMC - PubMed
    1. Messing J. Synergy of two reference genomes for the grass family. Plant Physiol. 2009;149:117–124. doi: 10.1104/pp.108.128520. - DOI - PMC - PubMed

Publication types

Associated data

LinkOut - more resources