Sequence composition and genome organization of maize

Messing, Joachim; Bharti, Arvind K.; Karłowski, Wojciech M.; Gundlach, Heidrun; Kim, Hye Ran; Yu, Yun William; Wei, Fusheng; Fuks, Galina; Soderlund, Carol; Mayer, Klaus; Wing, Rod A.

doi:10.1073/pnas.0406163101

Cited by 298 publications

(244 citation statements)

References 38 publications

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“…A notable characteristic of the predicted gene structures was the presence of numerous long introns (Fig. 1b), with mean intron length being higher than in most available plant genomes, although similar to the repeat-rich genomes of Vitis vinifera and Zea mays 17,18 . The longest intron in the high-confidence genes was 68 kb (Supplementary Table 2.6), and 2,384 high-confidence genes contained 2,880 longer than 5-kb introns (20 of which we confirmed by PCR amplification; Supplementary Information 2.14), 2,679 of which contained a repeat, suggesting that repeat insertions account for intron expansion.…”

Section: Presence Of Long Introns and Gene-like Fragmentsmentioning

confidence: 75%

The Norway spruce genome sequence and conifer genome evolution

Nystedt

Street

Wetterbom

et al. 2013

Nature

1,310

1,464

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Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

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Section: Presence Of Long Introns and Gene-like Fragmentsmentioning

confidence: 75%

The Norway spruce genome sequence and conifer genome evolution

Nystedt

Street

Wetterbom

et al. 2013

Nature

1,310

1,464

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“…In maize, for example, TEs comprise 60-80% of the genome (SanMiguel et al 1996;Messing et al 2004). The proportion is lower, but still substantial, in compact genomes like those of rice and Arabidopsis thaliana.…”

Section: Introductionmentioning

confidence: 99%

“…The proportion is lower, but still substantial, in compact genomes like those of rice and Arabidopsis thaliana. TEs represent 29% of the rice genome (Messing et al 2004) and 10% of the 125-Mb Arabidopsis genome (Arabidopsis Genome Initiative 2000). TEs are traditionally categorized into two groups based on their mode of transposition.…”

Section: Introductionmentioning

confidence: 99%

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

Lockton

Gaut

2009

J Mol Evol

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The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.

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“…However, the nucleotide contribution of class I is greater than that of class II, due mostly to the large size of LTR retrotransposons and the small size of IS5/Tourist and IS630/Tc1/mariner elements. The inverse is the case for maize, for which class I elements outnumber class II elements 42 . Given their larger sizes, differential amplification of LTR elements in maize compared with rice is consistent with the genomic expansion found between orthologous regions of rice and maize 15,33 .…”

Section: Transposable Elementsmentioning

confidence: 99%

The map-based sequence of the rice genome

Matsumoto¹,

Wu²,

Kanamori³

et al. 2005

Nature

3,316

1,017

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Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

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Sequence composition and genome organization of maize

Cited by 298 publications

References 38 publications

The Norway spruce genome sequence and conifer genome evolution

The Norway spruce genome sequence and conifer genome evolution

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The map-based sequence of the rice genome

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