Construction and Analysis of a Human-Chimpanzee Comparative Clone Map

Fujiyama, Asao; Watanabe, Hidemi; Toyoda, Atsushi; Taylor, Todd D.; Itoh, Takehiko; Tsai, Shih Feng; Park, Hong Seog; Yaspo, Marie Laure; Lehrach, Hans; Zhu, Chen; Fu, Gang; Saitou, Naruya; Osoegawa, Kazutoyo; Jong, Pieter J. de; Suto, Yumiko; Hattori, Masahira; Sakaki, Yoshiyuki

doi:10.1126/science.1065199

Cited by 220 publications

(151 citation statements)

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“…We did not observe significant correlations between the frequencies of base substitution and indels. Two large indel hotspots were found at around 9.5-11.5 Mb and 16.5-17.5 Mb from the centromere, as previously suggested 3,14 (Fig. 1b).…”

Section: Mapping Sequencing and Overview Of Ptr22supporting

confidence: 56%

“…The overall nucleotide substitution level in aligned regions between PTR22q and HSA21q is about 1.44% (excluding indels), which is significantly higher than the calculation based on high-quality BAC end sequence data (1.23%) 3 . Similar trends have also been observed for HSA21q based on smaller comparisons with the chimpanzee genome 18 .…”

Section: Base Substitutionsmentioning

confidence: 94%

“…The details concerning mapping and sequencing are summarized in Supplementary Tables 1 and 2 3 and PCR screening of expanded BAC libraries using highdensity human STS primers placed at roughly 20-kb intervals. Only the clones having multiple STS markers and sharing common STSs with neighbouring clones were considered as a member of a clone contig.…”

Section: Methodsmentioning

confidence: 99%

“…Estimates of nucleotide substitution rates of aligned sequences range from 1.23% by bacterial artificial chromosome (BAC) end sequencing 3 to about 2% by molecular analysis 1,[6][7][8] , whereas the overall sequence difference was estimated to be approximately 5% by taking regions of insertions or deletions (indels) into account 9 . Chromosomal rearrangements including duplications, translocations and transpositions have also been identified 10,11 .…”

mentioning

confidence: 99%

“…To understand the genetic basis of the unique features of humans, a number of pilot studies comparing the human and chimpanzee genomes have been conducted [1][2][3][4][5] . Estimates of nucleotide substitution rates of aligned sequences range from 1.23% by bacterial artificial chromosome (BAC) end sequencing 3 to about 2% by molecular analysis 1,[6][7][8] , whereas the overall sequence difference was estimated to be approximately 5% by taking regions of insertions or deletions (indels) into account 9 .…”

mentioning

confidence: 99%

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DNA sequence and comparative analysis of chimpanzee chromosome 22

Watanabe

Fujiyama²,

Hattori³

et al. 2004

Nature

209

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Human–chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized

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Section: Mapping Sequencing and Overview Of Ptr22supporting

confidence: 56%

Section: Base Substitutionsmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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DNA sequence and comparative analysis of chimpanzee chromosome 22

Watanabe

Fujiyama²,

Hattori³

et al. 2004

Nature

209

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Comparative analysis for mapping and sequence assembly

Milosavljevic

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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The increasing number of assembled reference sequences produced by ongoing genome sequencing projects provides information that is useful for the mapping and assembly of related genomes. Comparative information has the potential to both decrease the cost and accelerate mapping and sequencing projects by reducing experimental effort. Anchoring of contigs from one species onto an assembled genome of the other related species provides hypothetical order, orientation, and distance information. Mapping cloned genomic fragments, such as Bacterial Artificial Chromosomes (BACs), of one species onto an already assembled genome of another may be either used to select clones for targeted comparative sequencing or to infer the hypothetical order and orientation of BACs. Assembled genomic sequence of one species can be used as a template to guide the assembly of another, related species.

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