@ARTICLE{TreeBASE2Ref23211,
author = {Kathryn B Walters-Conte and Diana L.E. Johnson and warren e johnson and Stephen J. O'Brien and Jill Pecon-Slattery},
title = {The Dynamic Proliferation of CanSINEs Mirrors the Complex Evolution of Feliforms},
year = {2014},
keywords = {Felid SINE Genome},
doi = {},
url = {http://},
pmid = {},
journal = {BMC Evolutionary Biology},
volume = {},
number = {},
pages = {},
abstract = {Background: Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed.
Results: We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays.
Conclusions: We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement.
}
}
Taxa for matrix 22759 of Study 15822
Citation title:
"The Dynamic Proliferation of CanSINEs Mirrors the Complex Evolution of Feliforms".
Study name:
"The Dynamic Proliferation of CanSINEs Mirrors the Complex Evolution of Feliforms".
This study is part of submission 15822
(Status: Published).
Taxa
Return to matrix row view
ID |
Taxon Label |
NCBI taxid |
uBIO namebankID |
1520601 |
Caracal aurata 105890 |
|
|
1520573 |
Caracal caracal 133135 |
61394
|
2478140
|
1520586 |
Caracal serval 101187 |
|
|
1520648 |
Cryptoprocta ferox 131713 |
94188
|
2478432
|
1520640 |
Felidae sp. 122236 |
|
|
1520591 |
Felidae sp. 203464 |
|
|
1520594 |
Felidae sp. 214534 |
|
|
1520615 |
Feliformia sp. 101187 |
|
|
1520650 |
Feliformia sp. 106256 |
|
|
1520616 |
Feliformia sp. 107176 |
|
|
1520582 |
Feliformia sp. 117885 |
|
|
1520599 |
Feliformia sp. 131713 |
|
|
1520604 |
Feliformia sp. 134929 |
|
|
1520626 |
Feliformia sp. 135256 |
|
|
1520577 |
Feliformia sp. 136949 |
|
|
1520605 |
Feliformia sp. 145617 |
|
|
1520636 |
Feliformia sp. 145754 |
|
|
1520569 |
Feliformia sp. 150913 |
|
|
1520581 |
Feliformia sp. 151787 |
|
|
1520611 |
Feliformia sp. 164336 |
|
|
1520595 |
Feliformia sp. 174511 |
|
|
1520646 |
Feliformia sp. 179189 |
|
|
1520632 |
Feliformia sp. 180515 |
|
|
1520579 |
Feliformia sp. 194731 |
|
|
1520630 |
Feliformia sp. 199572 |
|
|
1520642 |
Feliformia sp. 203536 |
|
|
1520580 |
Feliformia sp. 206155 |
|
|
1520578 |
Feliformia sp. 212906 |
|
|
1520639 |
Feliformia sp. 213652 |
|
|
1520598 |
Feliformia sp. 217179 |
|
|
1520596 |
Feliformia sp. 4743 |
|
|
1520633 |
Feliformia sp. 95036 |
|
|
1520603 |
Feliformia sp. 95892 |
|
|
1520638 |
Feliformia sp. 99463 |
|
|
1520622 |
Feliformia sp. 99534 |
|
|
1520629 |
Felis nigripes 150951 |
61379
|
2478148
|
1520631 |
Felis nigripes 212075 |
61379
|
2478148
|
1520652 |
Felis nigripes 99643 |
61379
|
2478148
|
1520588 |
Felis silvestris silvestris 203464 |
9683
|
2635851
|
1520621 |
Felis sp. 105890 |
9687
|
10131575
|
1520644 |
Leopardus colocolo 122236 |
61406
|
10148347
|
1520589 |
Leopardus geoffroyi chD4.80M |
46844
|
5479004
|
1520613 |
Leopardus pardalis 150951 |
32538
|
2478153
|
1520575 |
Leopardus sp. 133135 |
|
|
1520607 |
Leopardus tigrinus 213798 |
46842
|
105482
|
1520619 |
Lynx canadensis 106256 |
61383
|
2478159
|
1520584 |
Lynx canadensis 73133 |
61383
|
2478159
|
1520583 |
Lynx lynx 204133 |
13125
|
2478160
|
1520653 |
Lynx pardinus 106256 |
191816
|
2478161
|
1520647 |
Lynx rufus 133135 |
61384
|
2478162
|
1520655 |
Lynx sp. 139216 |
|
|
1520618 |
Lynx sp. 154966 |
|
|
1520585 |
Neofelis neofelis 199572 |
|
|
1520574 |
Neofelis neofelis 212733 |
|
|
1520649 |
Otocolobus manul 105890 |
61408
|
2478170
|
1520606 |
Otocolobus manul 139216 |
61408
|
2478170
|
1520657 |
Otocolobus manul 212331 |
61408
|
2478170
|
1520609 |
Otocolobus manul 213566 |
61408
|
2478170
|
1520645 |
Otocolobus manul 215122 |
61408
|
2478170
|
1520635 |
Otocolobus manul 73133 |
61408
|
2478170
|
1520576 |
Panthera onca 5313 |
9690
|
2478186
|
1520610 |
Panthera onca chB1.32M |
9690
|
2478186
|
1520597 |
Panthera sp. 782 |
|
|
1520572 |
Panthera unica 134292 |
|
6318448
|
1520612 |
Pantherinae sp. chA1.248M |
|
|
1520651 |
Pardofelis badia 146417 |
|
10148359
|
1520624 |
Pardofelis badia 150162 |
|
10148359
|
1520654 |
Pardofelis marmorata 106256 |
61410
|
2478172
|
1520628 |
Pardofelis marmorata 133135 |
61410
|
2478172
|
1520623 |
Pardofelis marmorata 145617 |
61410
|
2478172
|
1520625 |
Pardofelis marmorata 150853 |
61410
|
2478172
|
1520592 |
Pardofelis marmorata 216162 |
61410
|
2478172
|
1520608 |
Pardofelis marmorata 216524 |
61410
|
2478172
|
1520620 |
Pardofelis sp. 212075 |
|
|
1520593 |
Prionailurus bengalensis 161275 |
37029
|
2478174
|
1520614 |
Prionailurus bengalensis 212075 |
37029
|
2478174
|
1520656 |
Prionailurus planiceps 212075 |
61403
|
2478175
|
1520571 |
Prionailurus sp. 130416 |
|
|
1520641 |
Prionailurus sp. 134463 |
|
|
1520600 |
Prionailurus sp. 150853 |
|
|
1520590 |
Prionailurus sp. 150951 |
|
|
1520643 |
Prionailurus sp. ch1.181M |
|
|
1520602 |
Prionailurus sp. chA1.248M |
|
|
1520570 |
Prionailurus viverrinus 125972 |
61388
|
2478177
|
1520634 |
Prionailurus viverrinus 164336 |
61388
|
2478177
|
1520627 |
Priondontidae 115304 |
|
|
1520587 |
Puma yagouaroundi 101187 |
61402
|
10148344
|
1520637 |
SINEC Fc R |
|
|
1520617 |
SINEC Fc2 |
|
|