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

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

doi:10.1186/1471-2229-10-116

Cited by 79 publications

(77 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…We predicted 31,987 protein-coding genes in the moso bamboo genome, with the support of RNA sequencing (RNA-seq) data (127 Gb) obtained from 7 bamboo tissues and 8,253 bamboo full-length cDNA sequences 2 Table 4). …”

Section: E T T E R Smentioning

confidence: 85%

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

et al. 2013

Self Cite

View full text Add to dashboard Cite

l e t t e r sBamboo represents the only major lineage of grasses that is native to forests and is one of the most important nontimber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between droughtresponsive and flowering genes.Bamboo is one of the most important non-timber forest products in the world. About 2.5 billion people depend economically on bamboo, and international trade in bamboo amounts to over 2.5 billion US dollars per year 1 . Bamboo has a rather striking life history, characterized by a prolonged vegetative phase lasting decades before flowering, thereby inhibiting genetic improvement. Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .Here, we report the draft genome of moso bamboo, a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area. Comparative genome-wide analyses of bamboo to other grass species, including rice, maize and sorghum, yielded new genetic insights into the rapid and marked phenotypic and ecological divergence of bamboo and closely related grasses.The moso bamboo genome contains 24 pairs of chromosomes 8 (2n = 48) and is characteristic of a diploid (Supplementary Fig. 1a). We conducted a flow cytometry analysis and estimated that it had a genome size of 2.075 Gb (2C = 4.24 pg; Supplementary Fig. 1b), which was very close to that estimated in a previous report 9 .Because it is difficult to generate an inbred line of moso bamboo, owing to its infrequent sexual reproduction and the long periods of time between flowering intervals, we selected five plants from a single individual rhizome of the moso bamboo ecotype (P. heterocycla var. pubescens) and performed whole-genome shotgun sequencing. We generated 295 Gb of raw sequence data (approximately 147-fold coverage), including Illumina short reads and 10,327 pairs of BAC end ...

show abstract

Section: E T T E R Smentioning

confidence: 85%

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

et al. 2013

Self Cite

View full text Add to dashboard Cite

show abstract

“…Some workers reported a (B,E)P relationship with Bambusoideae and Ehrhartoideae being more closely related than Pooideae (GPWG, 2001;Vicentini et al, 2008;Sungkaew et al, 2009). However, other studies proposed either an (E, P)B relationship (Mason-Gamer et al, 1998;Mathews et al, 2000) or a (B,P)E relationship (Zhang, 2000;Bouchenak-Khelladi et al, 2008;Leseberg and Duvall, 2009;Peng et al, 2010;Wu and Ge, 2012).…”

Section: Introductionmentioning

confidence: 90%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

View full text Add to dashboard Cite

Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

show abstract

“…It provides the first large sequence dataset for studying the structure and function of a substantial portion of bamboo genes, and fills the gap in the grass family for comparative genomics (Peng et al, 2010). In our study, TEs in the transcriptome were stringently scanned.…”

Section: Discussionmentioning

confidence: 99%

“…GenBank contains 10,608 P. pubescens FL-cDNAs, of which 4217 are expressed in leaf tissue, 3072 are expressed in embryos and 3318 are expressed in shoots (Peng et al, 2010). We investigated the distribution of the four most abundant TE families and found 24 Mutator, 11 Tc1/mariner, 15 Ty1-copia, and 15 Ty3-gypsy among these sequences.…”

Section: Analysis Of the Transcript Profiles Of Cdna-tesmentioning

confidence: 99%

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats

Zhou

Liu²,

Tang³

2011

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FLcDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and 3027 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 10 (4): 3026-3037 (2011) Structure and evolution of Phyllostachys pubescens genome CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.

show abstract

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

Cited by 79 publications

References 59 publications

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats

Contact Info

Product

Resources

About