@ARTICLE{TreeBASE2Ref25507,
author = {Yaoyao Cui and Chaochao Yan and Jing LI and Tianlin Sun and Bisong Yue and Xiuyue Zhang and Jing Li},
title = {Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny},
year = {2016},
keywords = {CR1 retroposons, repetitive elements, Arborophila rufipectus, Phasianidae, phylogeny},
doi = {10.1111/1755-0998.12514},
url = {http://},
pmid = {},
journal = {Molecular Ecology Resources},
volume = {},
number = {},
pages = {},
abstract = {Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In the present study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254,966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined dataset comprising of twenty two CR1 loci, mitochondrial genomes and eight unlinked introns was analyzed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.}
}
Citation for Study 18808
Citation title:
"Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny".
Study name:
"Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny".
This study is part of submission 18808
(Status: Published).
Citation
Cui Y., Yan C., Li J., Sun T., Yue B., Zhang X., & Li J. 2016. Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny. Molecular Ecology Resources, .
Authors
-
Cui Y.
(submitter)
18428391788
-
Yan C.
-
Li J.
-
Sun T.
15982219432
-
Yue B.
-
Zhang X.
-
Li J.
Abstract
Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In the present study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254,966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined dataset comprising of twenty two CR1 loci, mitochondrial genomes and eight unlinked introns was analyzed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.
Keywords
CR1 retroposons, repetitive elements, Arborophila rufipectus, Phasianidae, phylogeny
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S18808
- Other versions:
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NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref25507,
author = {Yaoyao Cui and Chaochao Yan and Jing LI and Tianlin Sun and Bisong Yue and Xiuyue Zhang and Jing Li},
title = {Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny},
year = {2016},
keywords = {CR1 retroposons, repetitive elements, Arborophila rufipectus, Phasianidae, phylogeny},
doi = {10.1111/1755-0998.12514},
url = {http://},
pmid = {},
journal = {Molecular Ecology Resources},
volume = {},
number = {},
pages = {},
abstract = {Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In the present study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254,966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined dataset comprising of twenty two CR1 loci, mitochondrial genomes and eight unlinked introns was analyzed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.}
}
- Show RIS reference
TY - JOUR
ID - 25507
AU - Cui,Yaoyao
AU - Yan,Chaochao
AU - LI,Jing
AU - Sun,Tianlin
AU - Yue,Bisong
AU - Zhang,Xiuyue
AU - Li,Jing
T1 - Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny
PY - 2016
KW - CR1 retroposons
KW - repetitive elements
KW - Arborophila rufipectus
KW - Phasianidae
KW - phylogeny
UR - http://dx.doi.org/10.1111/1755-0998.12514
N2 - Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In the present study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254,966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined dataset comprising of twenty two CR1 loci, mitochondrial genomes and eight unlinked introns was analyzed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.
L3 - 10.1111/1755-0998.12514
JF - Molecular Ecology Resources
VL -
IS -
ER -
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