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Patrick S. Schnable,
Doreen Ware,
Robert S. Fulton,
Joshua C. Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A. Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G. Presting,
Susan R. Wessler,
Srinivas Aluru,
Robert A. Martienssen,
Sandra W. Clifton,
W. Richard McCombie,
Rod A. Wing,
Richard K. Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for
biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of
the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were
responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions
of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven
gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state.
These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural
improvements of maize.
Science 11/2009; 326(5956):1112-1115. · 31.20 Impact Factor
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Patrick S. Schnable,
Doreen Ware,
Robert S. Fulton,
Joshua C. Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A. Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G. Presting,
Susan R. Wessler,
Srinivas Aluru,
Robert A. Martienssen,
Sandra W. Clifton,
W. Richard McCombie,
Rod A. Wing,
Richard K. Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for
biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of
the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were
responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions
of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven
gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state.
These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural
improvements of maize.
Science 11/2009; 326(5956):1112-1115. · 31.20 Impact Factor
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Fusheng Wei,
Joshua C Stein,
Chengzhi Liang,
Jianwei Zhang,
Robert S Fulton,
Regina S Baucom,
Emanuele De Paoli,
Shiguo Zhou,
Lixing Yang,
Yujun Han, [......],
Blake C Meyers,
Jeffrey L Bennetzen,
Robert A Martienssen,
W Richard McCombie,
Srinivas Aluru,
Sandra W Clifton,
Patrick S Schnable,
Doreen Ware,
Richard K Wilson,
Rod A Wing
[show abstract]
[hide abstract]
ABSTRACT: Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
PLoS Genetics 11/2009; 5(11):e1000728. · 8.69 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
PLoS Genetics 11/2009; 5(11):e1000716. · 8.69 Impact Factor
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Patrick S Schnable,
Doreen Ware,
Robert S Fulton,
Joshua C Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G Presting,
Susan R Wessler,
Srinivas Aluru,
Robert A Martienssen,
Sandra W Clifton,
W Richard McCombie,
Rod A Wing,
Richard K Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
Science 11/2009; 326(5956):1112-5. · 31.20 Impact Factor
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Andrew H. Paterson,
John E. Bowers,
R|[eacute]|my Bruggmann,
Inna Dubchak,
Jane Grimwood,
Heidrun Gundlach,
Georg Haberer,
Uffe Hellsten,
Therese Mitros,
Alexander Poliakov, [......],
Stephen Kresovich,
Maureen C. McCann,
Ray Ming,
Daniel G. Peterson,
Mehboob-ur-Rahman,
Doreen Ware,
Peter Westhoff,
Klaus F. X. Mayer,
Joachim Messing,
Daniel S. Rokhsar
[show abstract]
[hide abstract]
ABSTRACT: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the 730-megabase Sorghum bicolor (L.) Moench genome, placing 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization 70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
Nature 01/2009; 457(7229):551-556. · 36.28 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolution and are themselves an important subject of study. Repeat annotation, based on counting occurrences of k-mers, has been previously used to distinguish TEs from low-copy genic regions; but currently available software solutions are impractical due to high memory requirements or specialization for specific user-tasks.
Here we introduce the Tallymer software, a flexible and memory-efficient collection of programs for k-mer counting and indexing of large sequence sets. Unlike previous methods, Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particular, Tallymer was used to index a set of whole genome shotgun sequences from maize (B73) (total size 109 bp.). We analyzed k-mer frequencies for a wide range of k. At this low genome coverage ( approximately 0.45x) highly repetitive 20-mers constituted 44% of the genome but represented only 1% of all possible k-mers. Similar low-complexity was seen in the repeat fractions of sorghum and rice. When applying our method to other maize data sets, High-C0t derived sequences showed the greatest enrichment for low-copy sequences. Among annotated TEs, the most highly repetitive were of the Ty3/gypsy class of retrotransposons, followed by the Ty1/copia class, and DNA transposons. Among expressed sequence tags (EST), a notable fraction contained high-copy k-mers, suggesting that transposons are still active in maize. Retrotransposons in Mo17 and McC cultivars were readily detected using the B73 20-mer frequency index, indicating their conservation despite extensive rearrangement across cultivars. Among one hundred annotated bacterial artificial chromosomes (BACs), k-mer frequency could be used to detect transposon-encoded genes with 92% sensitivity, compared to 96% using alignment-based repeat masking, while both methods showed 92% specificity.
The Tallymer software was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available. For more information on the software, see http://www.zbh.uni-hamburg.de/Tallymer.
BMC Genomics 11/2008; 9:517. · 4.07 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences.
We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised.
An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be used across species is outweighed by the low costs of Illumina/Solexa sequencing which makes any chosen genome accessible for whole-genome sequence sampling.
BMC Genomics 02/2008; 9:518. · 4.07 Impact Factor
