Decoding the rice genome

Vij, Shubha; Gupta, Vikrant; Kumar, Dibyendu; Ravi, Vydianathan; Raghuvanshi, Saurabh; Khurana, Paramjit; Khurana, Jitendra P.; Tyagi, Akhilesh K.

doi:10.1002/bies.20399

Cited by 44 publications

(43 citation statements)

References 103 publications

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“…Rice (Oryza sativa) , until now the only monocot species with a genome sequence near completion, possesses a small genome (1C = 490 Mbp; Bennett and Smith, 1976) whose size is not very different from that of banana. Sequence analysis revealed that about 35% of the rice genome accounted for non-coding sequences (Vij et al, 2006). Provided that the number and size of banana genes do not differ significantly from rice, the banana genome should contain about 55% non-coding DNA accounting for about 300 Mbp.…”

Section: Resultsmentioning

confidence: 99%

Isolation and characterization of the highly repeated fraction of the banana genome

Hřibová

Doleželová²,

Town³

et al. 2007

Cytogenet Genome Res

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Although the nuclear genome of banana (Musa spp.) is relatively small (1C ∼ 610 Mbp for M. acuminata), the results obtained from other sequenced genomes suggest that more than half of the banana genome may be composed of repetitive and non-coding DNA sequences. Knowledge of repetitive DNA can facilitate mapping of important traits, phylogenetic studies, BAC-based physical mapping, and genome sequencing/annotation. However, only a few repetitive DNA sequences have been characterized in banana. In this work, we used DNA reassociation kinetics to isolate the highly repeated fraction of the banana genome (M. acuminata ‘Calcutta 4’). Two libraries, one prepared from Cot ≤0.05 DNA (2,688 clones) and one from Cot ≤0.1 sequences (4,608 clones), were constructed, and 614 DNA clones were chosen randomly for sequencing and further characterization. Dot-plot analysis revealed that 14% of the sequenced clones contained various semi-tandem and palindromic repeated sequences. ‘BLAST’ homology searches showed that, in addition to tandem repeats, the Cot libraries were composed mainly of different types of retrotransposons, the most frequent being the Ty3/gypsy type monkey retrotransposon. Selected sequences displaying tandem organization properties were mapped by PRimed IN Situ DNA labeling (PRINS) to the secondary constriction on metaphase chromosomes of M. acuminata ‘Calcutta 4’. Southern hybridization with selected BAC clones carrying 45S rDNA confirmed the presence of the tandem repeats in the 45S rDNA unit. This work significantly expands the knowledge of the repetitive fraction of the Musa genome and organization of its chromosomes.

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Section: Resultsmentioning

confidence: 99%

Isolation and characterization of the highly repeated fraction of the banana genome

Hřibová

Doleželová²,

Town³

et al. 2007

Cytogenet Genome Res

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“…A signiWcant amount of data have accumulated on gene annotation (The Rice Chromosome 3 Sequencing Consortium 2005), gene expression (Kikuchi et al 2003) and genome organization (The Rice Chromosome 3 Sequencing Consortium 2005; The Rice Chromosome 11 and 12 Sequencing Consortia 2005; Vij et al 2006) following completion of whole genome sequencing projects in rice (GoV et al 2002;Yu et al 2002;International Rice Genome Sequencing Project 2005). However, occurrence and distribution of microsatellites (tandemly repeated short DNA motifs) in the rice genome has not been a subject of high throughput research.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of conservation and divergence of microsatellites in rice

2009

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Studies on microsatellite distribution and divergence in related genomes contribute towards understanding of genome evolution in eukaryotes. Despite the availability of whole genome sequences of four rice genomes, occurrence and significance of microsatellites in the rice genome has remained a relatively unexplored area of research. We have aligned genomes of two rice subspecies i.e. indica and japonica to understand the trends of microsatellite conservation and divergence in the rice genome. Nearly 62% of the indica microsatellites were also found in the japonica genome. Occurrence of microsatellites showed a negative association with that of retrotransposons. Microsatellites repeat unit length and sequence showed direct influence on the microsatellite locus length. Further, microsatellite allele length was also influenced by the sequence characteristics of the neighbouring regions. CCG repeats were most conserved microsatellite sequences across the different syntenic regions in the two rice genomes and often showed association with CpG islands. Our study suggested that microsatellite distribution is not only governed by a balance between replication slippage and point mutations as proposed earlier, but also by the microsatellite motif sequence and characteristics of microsatellite neighbouring regions in the genome. Thus, this study is likely to prove an important reference for understanding the process of microsatellite evolution and dynamics in the two rice subspecies.

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“…It is likely that DNG701 is also involved in endosperm demethylation in rice and, unlike its Arabidopsis counterparts (DML2 and ROS1), targets developmentally important genes. Compared with Arabidopsis, the rice genome contains a substantially higher amount of transposons and other repetitive elements (25,26). Therefore, it is possible that more genes in rice are subject to regulatory control by repetitive elements, and thus more genes are likely targeted for demethylation by DNG701.…”

Section: Discussionmentioning

confidence: 99%

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

Ding

Mishra

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.Oryza sativa | incision activity | Tos17 copy number I n eukaryotes, DNA cytosine methylation at carbon 5 of the pyrimidine ring [5-methylcytosine (5-meC)] is an important epigenetic mark that contributes to gene silencing and plays critical roles in development and genome defense against viruses, transposons, and transgenes (1-3). Heavy cytosine methylation usually occurs at heterochromatin and at regions rich in transposons and repetitive DNA (2, 4). Cytosine methylation of DNA, however, is reversible through demethylation (5, 6). DNA demethylation can be passive or active, and active DNA demethylation is catalyzed by one or more enzymes to remove methylated cytosines and can occur independently of DNA replication (7,8). So far, several models have been proposed to explain mechanisms of DNA demethylation in animals (7,8). One of the models suggests that active DNA demethylation is mediated at least in part by a base excision repair (BER) pathway where the AID/Apobec family of deaminases convert 5-meC to T followed by G/T mismatch repair through the DNA glycosylase MBD4 or TDG with the involvement of Gadd45a (7-9). Recently, a new study suggested that 5-meC hydroxylase TET1 promotes DNA demethylation in mammalian cells through a process that requires the BER pathway (10). Nevertheless, many aspects of these models have not been confirmed, and how DNA demethylation is carried out in animals remains controversial (7,8).In contrast to the uncertainty about the mechanism of DNA demethylation in animals, mechanisms of DNA demethylation in plants are much clearer and widely accepted. In the model plant Arabidopsis, research showed that the 5-meC DNA glycosylase/ lyase-me...

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Decoding the rice genome

Cited by 44 publications

References 103 publications

Isolation and characterization of the highly repeated fraction of the banana genome

Isolation and characterization of the highly repeated fraction of the banana genome

Genome-wide analysis of conservation and divergence of microsatellites in rice

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

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