Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

Chen, Z Q; Ritzel, R. Gary; Lin, Chyi-Chyang; Hodgetts, Ross B.

doi:10.1073/pnas.88.13.5814

Cited by 33 publications

(16 citation statements)

References 22 publications

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“…CR1 elements are often associated with genes, notably in the ß-globin region (Reitman et al, 1993), and are typically orientated to point toward the expressed gene (Stumph et al, 1984). At present too little extensive chicken genomic sequence is available to define the relationship between CR1 sequences and genes but it is possible they play a role in regulation of expression (Chen, 1991).…”

Section: Genomic Sequencing (Prepared By N Bumstead and J Kaufman)mentioning

confidence: 99%

First report on chicken genes and chromosomes 2000

Schmid¹,

Nanda²,

Guttenbach³

et al. 2000

Cytogenet Genome Res

333

328

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Section: Genomic Sequencing (Prepared By N Bumstead and J Kaufman)mentioning

confidence: 99%

First report on chicken genes and chromosomes 2000

Schmid¹,

Nanda²,

Guttenbach³

et al. 2000

Cytogenet Genome Res

333

328

View full text Add to dashboard Cite

“…The case for studying retroelements in birds is being primed by completion of the chicken genome and, in particular, the characterization of CR1 retrotransposons, a large family of mobile chicken repeats that appear to be distributed widely among vertebrates (Chen et al 1991;Burch et al 1993;International Chicken Genome Sequencing Consortium 2004). CR1s were originally considered SINEs based on the extensive truncation of their 5 0 ends; however, longer CR1s have now been identified that contain the characteristic open reading frames of LINEs.…”

Section: The Future: the Tools Of Phylogenomics (A) Contiguous Versusmentioning

confidence: 99%

Phylogenetics of modern birds in the era of genomics

2005

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In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a 'community genomics' approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era-with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters-will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.

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“…The turtle and alligator species investigated here have environmental as opposed to genetic sex determination, and sex determination in Anolis is inferred to be genetic based on some karyological evidence (11). Several retroelement lineages have been characterized in turtles and other reptiles (12)(13)(14)(15). Projects in progress will produce genome sequences for another bird, the Zebra Finch, Taeniopygia guttata, and a lizard, Anolis carolinensis.…”

mentioning

confidence: 99%

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

Shedlock

Botka

Zhao³

et al. 2007

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

129

159

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We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of Ϸ65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.BAC ͉ Reptilia ͉ retroelement ͉ isochore ͉ intron

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Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

Cited by 33 publications

References 22 publications

First report on chicken genes and chromosomes 2000

First report on chicken genes and chromosomes 2000

Phylogenetics of modern birds in the era of genomics

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

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