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Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
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Suh A, Bachg S, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J. De-novo emergence of SINE retroposons during the early evolution of passerine birds. Mob DNA 2017; 8:21. [PMID: 29255493 PMCID: PMC5729268 DOI: 10.1186/s13100-017-0104-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. RESULTS Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. CONCLUSIONS We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Department of Evolutionary Biology (EBC), Uppsala University, SE-75236 Uppsala, Sweden
| | - Sandra Bachg
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
| | - Stephen Donnellan
- South Australian Museum, Adelaide, SA 5000 Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005 Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601 Australia
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Brandenburg Medical School (MHB), D-16816 Neuruppin, Germany
| | - Jan Ole Kriegs
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- LWL-Museum für Naturkunde, Westfälisches Landesmuseum mit Planetarium, D-48161 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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3
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Gao B, Wang S, Wang Y, Shen D, Xue S, Chen C, Cui H, Song C. Low diversity, activity, and density of transposable elements in five avian genomes. Funct Integr Genomics 2017; 17:427-439. [PMID: 28190211 PMCID: PMC5486457 DOI: 10.1007/s10142-017-0545-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 12/16/2016] [Accepted: 01/30/2017] [Indexed: 11/29/2022]
Abstract
In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.
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Affiliation(s)
- Bo Gao
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Saisai Wang
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Yali Wang
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Dan Shen
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Songlei Xue
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Hengmi Cui
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Chengyi Song
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
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4
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Cui Y, Yan C, Sun T, Li J, Yue B, Zhang X, Li J. Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny. Mol Ecol Resour 2016; 16:1037-49. [PMID: 26929266 DOI: 10.1111/1755-0998.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022]
Abstract
Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In this 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 data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed 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.
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Affiliation(s)
- Yaoyao Cui
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Chaochao Yan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Tianlin Sun
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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6
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Haddrath O, Baker AJ. Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proc Biol Sci 2012; 279:4617-25. [PMID: 22977150 DOI: 10.1098/rspb.2012.1630] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122-138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada.
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7
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CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes). Gene 2012; 502:125-32. [PMID: 22565186 DOI: 10.1016/j.gene.2012.04.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 04/20/2012] [Accepted: 04/22/2012] [Indexed: 01/21/2023]
Abstract
Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.
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8
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Suh A, Kriegs JO, Donnellan S, Brosius J, Schmitz J. A universal method for the study of CR1 retroposons in nonmodel bird genomes. Mol Biol Evol 2012; 29:2899-903. [PMID: 22522308 DOI: 10.1093/molbev/mss124] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
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9
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Matzke A, Churakov G, Berkes P, Arms EM, Kelsey D, Brosius J, Kriegs JO, Schmitz J. Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era. Mol Biol Evol 2012; 29:1497-501. [PMID: 22319163 DOI: 10.1093/molbev/msr319] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
More than 150 Ma, the avian lineage separated from that of other dinosaurs and later diversified into the more than 10,000 species extant today. The early neoavian bird radiations most likely occurred in the late Cretaceous (more than 65 Ma) but left behind few if any molecular signals of their archaic evolutionary past. Retroposed elements, once established in an ancestral population, are highly valuable, virtually homoplasy-free markers of species evolution; after applying stringent orthology criteria, their phylogenetically informative presence/absence patterns are free of random noise and independent of evolutionary rate or nucleotide composition effects. We screened for early neoavian orthologous retroposon insertions and identified six markers with conflicting presence/absence patterns, whereas six additional retroposons established before or after the presumed major neoavian radiation show consistent phylogenetic patterns. The exceptionally frequent conflicting retroposon presence/absence patterns of neoavian orders are strong indicators of an extensive incomplete lineage sorting era, potentially induced by an early rapid successive speciation of ancestral Neoaves.
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Han KL, Braun EL, Kimball RT, Reddy S, Bowie RCK, Braun MJ, Chojnowski JL, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. Are transposable element insertions homoplasy free?: an examination using the avian tree of life. Syst Biol 2011; 60:375-86. [PMID: 21303823 DOI: 10.1093/sysbio/syq100] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA.
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11
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Plötner J, Köhler F, Uzzell T, Beerli P, Schreiber R, Guex GD, Hotz H. Evolution of serum albumin intron-1 is shaped by a 5' truncated non-long terminal repeat retrotransposon in western Palearctic water frogs (Neobatrachia). Mol Phylogenet Evol 2009; 53:784-91. [PMID: 19665056 DOI: 10.1016/j.ympev.2009.07.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
A 5' truncated non-LTR CR1-like retrotransposon, named RanaCR1, was identified in the serum albumin intron-1 (SAI-1) of at least seven species of western Palearctic water frogs (WPWF). Based on sequence similarity of the carboxy-terminal region (CTR) of ORF2 and/or the highly conserved 3' untranslated region (3' UTR), RanaCR1-like elements occur also in the genome of Xenopus tropicalis and Rana temporaria. Unlike other CR1 elements, RanaCR1 contains a CA microsatellite in its 3' UTR. The low nucleotide diversity of the 3' UTR compared to the CTR and to SAI-1 suggests that this region still plays a role in WPWF, either as a structure-stabilizing element, or within a species-specific transcriptional network. Length variation of water frog SAI-1 sequences is caused by deletions that extend in some cases beyond the 5' or 3' ends of RanaCR1, probably a result of selection for structural and functional stability of the primary transcript. The impact of RanaCR1 on SAI-1 evolution is also indicated by the significant negative correlation between the length of both SAI-1 and RanaCR1 and the percentage GC content of RanaCR1. Both SAI-1 and RanaCR1 sequences support the sister group relationship of R. perezi and R. saharica, which are placed in the phylogenetic tree at a basal position, the sister clade to other water frog taxa. It also supports the monophyly of the R. lessonae group; of Anatolian water frogs (R. cf. bedriagae), which are not conspecific with R. bedriagae, and of the European ridibunda group. Within the ridibunda clade, Greek frogs are clearly separated, supporting the hypothesis that Balkan water frogs represent a distinct species. Frogs from Atyrau (Kazakhstan), the type locality of R. ridibunda, were heterozygous for a ridibunda and a cf. bedriagae specific allele.
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Affiliation(s)
- Jörg Plötner
- Museum für Naturkunde, Leibniz-Institut für Evolutions - und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, 10115 Berlin, Germany.
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12
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Schröder C, Bleidorn C, Hartmann S, Tiedemann R. Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives. Gene 2009; 448:221-6. [PMID: 19563867 DOI: 10.1016/j.gene.2009.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/18/2009] [Accepted: 06/18/2009] [Indexed: 02/07/2023]
Abstract
Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (dog-like carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony-informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.
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Affiliation(s)
- Christiane Schröder
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 26, 14476 Potsdam, Germany.
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13
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Liu GE, Jiang L, Tian F, Zhu B, Song J. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats. Genome Biol Evol 2009; 1:119-30. [PMID: 20333183 PMCID: PMC2817409 DOI: 10.1093/gbe/evp014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2009] [Indexed: 11/12/2022] Open
Abstract
Chicken Repeat 1 (CR1) repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for approximately 80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 subfamilies as previously reported in Repbase. We performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the chicken genome. We identified and validated 57 chicken CR1 subfamilies and further analyzed the correlation between these subfamilies and their regional GC contents. We also discovered one novel lineage-specific CR1 subfamilies in turkeys when compared with chickens. We built an evolutionary tree of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.
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Affiliation(s)
- George E Liu
- Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA.
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14
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Treplin S, Siegert R, Bleidorn C, Thompson HS, Fotso R, Tiedemann R. Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00178.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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