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1.
PLoS Genet ; 5(11): e1000715, 2009 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-19936061

RESUMO

Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map ( approximately 1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1).


Assuntos
Genoma de Planta/genética , Zea mays/genética , Algoritmos , Sequência de Bases , Cromossomos Artificiais Bacterianos/genética , Cromossomos de Plantas/genética , Clonagem Molecular , Mapeamento de Sequências Contíguas , Marcadores Genéticos , Dados de Sequência Molecular , Fenômenos Ópticos , Mapeamento Físico do Cromossomo , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico
2.
PLoS Genet ; 5(11): e1000728, 2009 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-19936048

RESUMO

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.


Assuntos
Pareamento de Bases/genética , Genoma de Planta/genética , Zea mays/genética , Sequência de Bases , Cromossomos de Plantas/genética , Elementos de DNA Transponíveis/genética , Evolução Molecular , Duplicação Gênica , Rearranjo Gênico/genética , Genes de Plantas , Loci Gênicos/genética , Dados de Sequência Molecular , Mutação/genética , Fases de Leitura Aberta/genética , Oryza/genética , Mapeamento Físico do Cromossomo , RNA de Plantas/genética , Homologia de Sequência do Ácido Nucleico , Sorghum/genética , Sintenia/genética
3.
Nature ; 424(6945): 157-64, 2003 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-12853948

RESUMO

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.


Assuntos
Cromossomos Humanos Par 7 , Animais , Sequência de Bases , Duplicação Gênica , Humanos , Camundongos , Dados de Sequência Molecular , Mapeamento Físico do Cromossomo , Proteínas/genética , Pseudogenes , RNA não Traduzido , Análise de Sequência de DNA , Especificidade da Espécie , Síndrome de Williams/genética
5.
Nat Genet ; 45(9): 1083-7, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23872635

RESUMO

We compared the human and mouse X chromosomes to systematically test Ohno's law, which states that the gene content of X chromosomes is conserved across placental mammals. First, we improved the accuracy of the human X-chromosome reference sequence through single-haplotype sequencing of ampliconic regions. The new sequence closed gaps in the reference sequence, corrected previously misassembled regions and identified new palindromic amplicons. Our subsequent analysis led us to conclude that the evolution of human and mouse X chromosomes was bimodal. In accord with Ohno's law, 94-95% of X-linked single-copy genes are shared by humans and mice; most are expressed in both sexes. Notably, most X-ampliconic genes are exceptions to Ohno's law: only 31% of human and 22% of mouse X-ampliconic genes had orthologs in the other species. X-ampliconic genes are expressed predominantly in testicular germ cells, and many were independently acquired since divergence from the common ancestor of humans and mice, specializing portions of their X chromosomes for sperm production.


Assuntos
Células Germinativas/metabolismo , Cromossomo X/genética , Animais , Mapeamento Cromossômico , Biologia Computacional , Evolução Molecular , Genes Ligados ao Cromossomo X , Genômica , Humanos , Masculino , Mamíferos/genética , Camundongos , Dados de Sequência Molecular , Análise de Sequência de DNA , Cromossomo X/química
6.
Science ; 326(5956): 1112-5, 2009 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-19965430

RESUMO

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.


Assuntos
Variação Genética , Genoma de Planta , Análise de Sequência de DNA , Zea mays/genética , Sequência de Bases , Centrômero/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Produtos Agrícolas/genética , Variações do Número de Cópias de DNA , Metilação de DNA , Elementos de DNA Transponíveis , DNA de Plantas/genética , Genes de Plantas , Endogamia , MicroRNAs/genética , Dados de Sequência Molecular , Ploidias , RNA de Plantas/genética , Recombinação Genética , Retroelementos
7.
Nature ; 423(6942): 825-37, 2003 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-12815422

RESUMO

The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.


Assuntos
Cromossomos Humanos Y/genética , Evolução Molecular , Processos de Determinação Sexual , Transducina , Cromossomos Humanos X/genética , Troca Genética/genética , Elementos de DNA Transponíveis/genética , Eucromatina/genética , Feminino , Amplificação de Genes/genética , Conversão Gênica/genética , Genes/genética , Heterocromatina/genética , Humanos , Hibridização in Situ Fluorescente , Masculino , Modelos Genéticos , Família Multigênica/genética , Especificidade de Órgãos , Pseudogenes/genética , Homologia de Sequência do Ácido Nucleico , Caracteres Sexuais , Especificidade da Espécie , Testículo/metabolismo , Transcrição Gênica/genética
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