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Song B, Buckler ES, Stitzer MC. New whole-genome alignment tools are needed for tapping into plant diversity. TRENDS IN PLANT SCIENCE 2024; 29:355-369. [PMID: 37749022 DOI: 10.1016/j.tplants.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.
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Affiliation(s)
- Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China; Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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2
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Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
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Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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3
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Falcon F, Tanaka EM, Rodriguez-Terrones D. Transposon waves at the water-to-land transition. Curr Opin Genet Dev 2023; 81:102059. [PMID: 37343338 DOI: 10.1016/j.gde.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
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Affiliation(s)
- Francisco Falcon
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria. https://twitter.com/@FcoJFalcon
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| | - Diego Rodriguez-Terrones
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
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4
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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5
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Mezzasalma M, Capriglione T, Kupriyanova L, Odierna G, Pallotta MM, Petraccioli A, Picariello O, Guarino FM. Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome of Zootoca vivipara (Squamata, Lacertidae). Life (Basel) 2023; 13:life13030637. [PMID: 36983793 PMCID: PMC10058329 DOI: 10.3390/life13030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Transposable elements (TEs) constitute a considerable fraction of eukaryote genomes representing a major source of genetic variability. We describe two DNA sequences isolated in the lizard Zootoca vivipara, here named Zv516 and Zv817. Both sequences are single-copy nuclear sequences, including a truncation of two transposable elements (TEs), SINE Squam1 in Zv516 and a Tc1/Mariner-like DNA transposon in Zv817. FISH analyses with Zv516 showed the occurrence of interspersed signals of the SINE Squam1 sequence on all chromosomes of Z. vivipara and quantitative dot blot indicated that this TE is present with about 4700 copies in the Z. vivipara genome. FISH and dot blot with Zv817 did not produce clear hybridization signals. Bioinformatic analysis showed the presence of active SINE Squam 1 copies in the genome of different lacertids, in different mRNAs, and intronic and coding regions of various genes. The Tc1/Mariner-like DNA transposon occurs in all reptiles, excluding Sphenodon and Archosauria. Zv817 includes a trait of 284 bp, representing an amniote ultra-conserved element (UCE). Using amniote UCE homologous sequences from available whole genome sequences of major amniote taxonomic groups, we performed a phylogenetic analysis which retrieved Prototheria as the sister group of Metatheria and Eutheria. Within diapsids, Testudines are the sister group to Aves + Crocodylia (Archosauria), and Sphenodon is the sister group to Squamata. Furthermore, large trait regions flanking the UCE are conserved at family level.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (G.O.)
| | - Teresa Capriglione
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Larissa Kupriyanova
- Zoological Institute, Russian Academy of Sciences, 190121 St. Petersburg, Russia
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
- Correspondence: (M.M.); (G.O.)
| | | | - Agnese Petraccioli
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Orfeo Picariello
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Fabio M. Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy
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6
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Snetkova V, Pennacchio LA, Visel A, Dickel DE. Perfect and imperfect views of ultraconserved sequences. Nat Rev Genet 2022; 23:182-194. [PMID: 34764456 PMCID: PMC8858888 DOI: 10.1038/s41576-021-00424-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 12/12/2022]
Abstract
Across the human genome, there are nearly 500 'ultraconserved' elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes. Remarkably, the majority of these sequences are non-coding, and many can function as enhancers that activate tissue-specific gene expression during embryonic development. From their first description more than 15 years ago, their extreme conservation has both fascinated and perplexed researchers in genomics and evolutionary biology. The intrigue around ultraconserved elements only grew with the observation that they are dispensable for viability. Here, we review recent progress towards understanding the general importance and the specific functions of ultraconserved sequences in mammalian development and human disease and discuss possible explanations for their extreme conservation.
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Affiliation(s)
- Valentina Snetkova
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Len A. Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA,Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA,To whom correspondence should be addressed: L.A.P., ; A.V., ; D.E.D., (lead contact)
| | - Axel Visel
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Diane E. Dickel
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA,To whom correspondence should be addressed: L.A.P., ; A.V., ; D.E.D., (lead contact)
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7
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Cano-Sánchez E, Rodríguez-Gómez F, Ruedas LA, Oyama K, León-Paniagua L, Mastretta-Yanes A, Velazquez A. Using Ultraconserved Elements to Unravel Lagomorph Phylogenetic Relationships. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09595-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Akhlaghpour H. An RNA-Based Theory of Natural Universal Computation. J Theor Biol 2021; 537:110984. [PMID: 34979104 DOI: 10.1016/j.jtbi.2021.110984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signaling cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions relative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computational problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.
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Affiliation(s)
- Hessameddin Akhlaghpour
- Laboratory of Integrative Brain Function, The Rockefeller University, New York, NY, 10065, USA
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9
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Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Mol Ecol Resour 2021; 22:1100-1119. [PMID: 34569723 DOI: 10.1111/1755-0998.13517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022]
Abstract
Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.
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Affiliation(s)
- Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Kerry A Cobb
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Daniel M Portik
- California Academy of Sciences, San Francisco, California, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA.,Department of Biological Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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10
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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11
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McLaughlin JF, Faircloth BC, Glenn TC, Winker K. Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds. Mol Ecol 2020; 29:3526-3542. [PMID: 32745340 DOI: 10.1111/mec.15574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022]
Abstract
Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.
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Affiliation(s)
- Jessica F McLaughlin
- University of Alaska Museum, Fairbanks, AK, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Travis C Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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12
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Habic A, Mattick JS, Calin GA, Krese R, Konc J, Kunej T. Genetic Variations of Ultraconserved Elements in the Human Genome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:549-559. [PMID: 31689173 DOI: 10.1089/omi.2019.0156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ultraconserved elements (UCEs) are among the most popular DNA markers for phylogenomic analysis. In at least three of five placental mammalian genomes (human, dog, cow, mouse, and rat), 2189 UCEs of at least 200 bp in length that are identical have been identified. Most of these regions have not yet been functionally annotated, and their associations with diseases remain largely unknown. This is an important knowledge gap in human genomics with regard to UCE roles in physiologically critical functions, and by extension, their relevance for shared susceptibilities to common complex diseases across several mammalian organisms in the event of their polymorphic variations. In the present study, we remapped the genomic locations of these UCEs to the latest human genome assembly, and examined them for documented polymorphisms in sequenced human genomes. We identified 29,983 polymorphisms within analyzed UCEs, but revealed that a vast majority exhibits very low minor allele frequencies. Notably, only 112 of the identified polymorphisms are associated with a phenotype in the Ensembl genome browser. Through literature analyses, we confirmed associations of 37 (i.e., out of the 112) polymorphisms within 23 UCEs with 25 diseases and phenotypic traits, including, muscular dystrophies, eye diseases, and cancers (e.g., familial adenomatous polyposis). Most reports of UCE polymorphism-disease associations appeared to be not cognizant that their candidate polymorphisms were actually within UCEs. The present study offers strategic directions and knowledge gaps for future computational and experimental work so as to better understand the thus far intriguing and puzzling role(s) of UCEs in mammalian genomes.
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Affiliation(s)
- Anamarija Habic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - John S Mattick
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia.,Green Templeton College, University of Oxford, Oxford, United Kingdom
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,The Center for RNA Interference and Noncoding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Rok Krese
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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13
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Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour 2020; 20:892-905. [PMID: 32243090 PMCID: PMC7497042 DOI: 10.1111/1755-0998.13160] [Citation(s) in RCA: 453] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Alex Schomaker-Bastos
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonathan Romiguier
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Francisco Prosdocimi
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
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14
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Onimaru K. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species. Dev Growth Differ 2020; 62:326-333. [DOI: 10.1111/dgd.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Koh Onimaru
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research (BDR) Wako CitySaitama Japan
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15
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Casanova EL, Konkel MK. The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. Bioessays 2020; 42:e1900173. [PMID: 31943266 DOI: 10.1002/bies.201900173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes-often derived from transposable elements-drives punctuated bursts of morphological divergence and speciation across metazoa. This two-part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once-controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs.
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Affiliation(s)
- Emily L Casanova
- Department of Biomedical Sciences, University of South Carolina School of Medicine at Greenville, 200A Patewood Dr., Greenville, SC, 29615, USA
| | - Miriam K Konkel
- Department of Genetics, Clemson Center for Human Genetics, Biomedical Data Science and Informatics Program, Clemson University, 105 Collings St., Clemson, SC, 29631, USA
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16
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Pierce MP. Filling in the Gaps: Adopting Ultraconserved Elements Alongside COI to Strengthen Metabarcoding Studies. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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White ND, Braun MJ. Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores). Mol Phylogenet Evol 2019; 141:106611. [DOI: 10.1016/j.ympev.2019.106611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
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18
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Winker K, Glenn TC, Faircloth BC. Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. PeerJ 2018; 6:e5735. [PMID: 30310754 PMCID: PMC6174879 DOI: 10.7717/peerj.5735] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/05/2018] [Indexed: 01/08/2023] Open
Abstract
Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay's buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18-74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (F ST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500-240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8-5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum & Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Travis C. Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
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19
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The State of Long Non-Coding RNA Biology. Noncoding RNA 2018; 4:ncrna4030017. [PMID: 30103474 PMCID: PMC6162524 DOI: 10.3390/ncrna4030017] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022] Open
Abstract
Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure–function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.
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20
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Edwards SV, Cloutier A, Baker AJ. Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics. Syst Biol 2017; 66:1028-1044. [PMID: 28637293 PMCID: PMC5790140 DOI: 10.1093/sysbio/syx058] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.
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Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
| | - Allan J. Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
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21
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Lai X, Behera S, Liang Z, Lu Y, Deogun JS, Schnable JC. STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species. MOLECULAR PLANT 2017; 10:990-999. [PMID: 28602693 DOI: 10.1016/j.molp.2017.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences (CNSs) based on alignment have had relatively large minimum sequence lengths (≥15 bp) compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.
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Affiliation(s)
- Xianjun Lai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Sairam Behera
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Zhikai Liang
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| | - James C Schnable
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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22
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Deveson IW, Hardwick SA, Mercer TR, Mattick JS. The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome. Trends Genet 2017; 33:464-478. [PMID: 28535931 DOI: 10.1016/j.tig.2017.04.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023]
Abstract
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.
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Affiliation(s)
- Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Simon A Hardwick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - John S Mattick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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23
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Abstract
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci. Parsing and characterizing the functions of noncoding RNAs-lncRNAs in particular-is one of the great challenges of modern genome biology. Here we discuss concepts and computational methods for the identification of structural domains in lncRNAs from genomic and transcriptomic data. In the first part, we briefly review how to identify RNA structural motifs in individual lncRNAs. In the second part, we describe how to leverage the evolutionary dynamics of structured RNAs in a computationally efficient screen to detect putative functional lncRNA motifs using comparative genomics.
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Affiliation(s)
- Martin A Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia. .,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia.
| | - John S Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia
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24
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Rubanov LI, Seliverstov AV, Zverkov OA, Lyubetsky VA. A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata. BMC Bioinformatics 2016; 17:385. [PMID: 27645252 PMCID: PMC5028923 DOI: 10.1186/s12859-016-1257-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/13/2016] [Indexed: 01/24/2023] Open
Abstract
Background Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between apicomplexans can be very high, in particular, due to the positive selection pressure on them. This complicates the identification of highly conserved elements in alveolates, which is overcome by the proposed algorithm. Results A novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed. Conclusion We proposed an algorithm for the identification of highly conserved elements. The multitude of identified elements was used to infer the phylogeny of Alveolata. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1257-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lev I Rubanov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia.
| | - Alexandr V Seliverstov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
| | - Oleg A Zverkov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
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25
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Polychronopoulos D, Athanasopoulou L, Almirantis Y. Fractality and entropic scaling in the chromosomal distribution of conserved noncoding elements in the human genome. Gene 2016; 584:148-60. [DOI: 10.1016/j.gene.2016.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/22/2016] [Accepted: 02/14/2016] [Indexed: 11/15/2022]
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26
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Hawkins MTR, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE. Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. BMC Evol Biol 2016; 16:80. [PMID: 27075887 PMCID: PMC4831120 DOI: 10.1186/s12862-016-0650-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melissa T R Hawkins
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA. .,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA. .,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, 22030, USA.
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana(EBD-CSIC), 41092, Sevilla, Spain
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Molly M McDonough
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Larry L Rockwood
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Jesus E Maldonado
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
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27
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McCormack JE, Tsai WLE, Faircloth BC. Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Resour 2015; 16:1189-203. [PMID: 26391430 DOI: 10.1111/1755-0998.12466] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/19/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023]
Abstract
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.
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Affiliation(s)
- John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
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28
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Yousaf A, Sohail Raza M, Ali Abbasi A. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. Genome Biol Evol 2015; 7:2333-43. [PMID: 26253316 PMCID: PMC4558863 DOI: 10.1093/gbe/evv146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates’ conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water–land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods’ enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land.
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Affiliation(s)
- Aisha Yousaf
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Sohail Raza
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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29
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Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. Mol Phylogenet Evol 2015; 92:140-6. [PMID: 26079130 DOI: 10.1016/j.ympev.2015.05.027] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 02/04/2023]
Abstract
Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.
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Affiliation(s)
- Princess S Gilbert
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | - Jonathan Chang
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine, University of California, Los Angeles, CA, USA
| | - Eric M Sobel
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Janet S Sinsheimer
- Department of Biomathematics, University of California, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Biostatistics, University of California, Los Angeles, CA, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Michael E Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
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30
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Lareau LF, Brenner SE. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Mol Biol Evol 2015; 32:1072-9. [PMID: 25576366 PMCID: PMC4379411 DOI: 10.1093/molbev/msv002] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ultraconserved elements, unusually long regions of perfect sequence identity, are found in genes encoding numerous RNA-binding proteins including arginine-serine rich (SR) splicing factors. Expression of these genes is regulated via alternative splicing of the ultraconserved regions to yield mRNAs that are degraded by nonsense-mediated mRNA decay (NMD), a process termed unproductive splicing (Lareau et al. 2007; Ni et al. 2007). As all human SR genes are affected by alternative splicing and NMD, one might expect this regulation to have originated in an early SR gene and persisted as duplications expanded the SR family. But in fact, unproductive splicing of most human SR genes arose independently (Lareau et al. 2007). This paradox led us to investigate the origin and proliferation of unproductive splicing in SR genes. We demonstrate that unproductive splicing of the splicing factor SRSF5 (SRp40) is conserved among all animals and even observed in fungi; this is a rare example of alternative splicing conserved between kingdoms, yet its effect is to trigger mRNA degradation. As the gene duplicated, the ancient unproductive splicing was lost in paralogs, and distinct unproductive splicing evolved rapidly and repeatedly to take its place. SR genes have consistently employed unproductive splicing, and while it is exceptionally conserved in some of these genes, turnover in specific events among paralogs shows flexible means to the same regulatory end.
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Affiliation(s)
- Liana F Lareau
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley Department of Biochemistry, Stanford University School of Medicine
| | - Steven E Brenner
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley
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31
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Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 2014; 346:1254449. [PMID: 25504731 PMCID: PMC4386873 DOI: 10.1126/science.1254449] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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Affiliation(s)
- Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Joel Armstrong
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Dent Earl
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Ngan Nguyen
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Glenn Hickey
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - John A St John
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Colin Kern
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jerzy Jurka
- Genetic Information Research Institute, Mountain View, CA 94043, USA
| | - Kenji K Kojima
- Genetic Information Research Institute, Mountain View, CA 94043, USA
| | | | | | - Arian F Smit
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Christine A Lavoie
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Meganathan P Ramakodi
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - John W Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Sally R Isberg
- Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, Australia
| | - Lee Miles
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Amanda Y Chong
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christopher Moran
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - John McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA
| | - Shane C Burgess
- College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Christina Williams
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Jason T Howard
- Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cathy R Gresham
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Erich D Jarvis
- Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher A Brochu
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
| | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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32
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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014; 346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Citation(s) in RCA: 1095] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
| | - Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andre J Aberer
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Bo Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Benoit Nabholz
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Claudia C Weber
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jianwen Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Nitish Narula
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ganesh Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Volodymyr Zavidovych
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Bhanu Rekepalli
- Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bent Lindow
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA
| | - David Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Richard E Green
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maria Paula Cruz Schneider
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil
| | - Francisco Prosdocimi
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - José Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Amhed Missael Vargas Velazquez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bent Petersen
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Ponten
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - An Pas
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Tom Bailey
- Dubai Falcon Hospital, Dubai, United Arab Emirates
| | - Paul Scofield
- Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia
| | - Amy C Driskell
- Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Zijun Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yongli Zeng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenyu Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Binghang Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiong Yinqi
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuemei Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Michael Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA
| | - Jon Fjeldsa
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Warren Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Stephen O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - John McCormack
- Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Dave Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany
| | - David P Mindell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wang Jun
- BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers. Genomics 2014; 104:79-86. [PMID: 25058025 DOI: 10.1016/j.ygeno.2014.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/15/2014] [Indexed: 12/29/2022]
Abstract
Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes. Here we present the analysis of CNEs with a methodology that takes into account word occurrence at various lengths scales in the form of feature vector representation and rule based classifiers. We implement our approach on both protein-coding exons and CNEs, originating from human, insect (Drosophila melanogaster) and worm (Caenorhabditis elegans) genomes, that are either identified in the present study or obtained from the literature. Alignment free feature vector representation of sequences combined with rule-based classification methods leads to successful classification of the different CNEs classes. Biologically meaningful results are derived by comparison with the genomic signatures approach, and classification rates for a variety of functional elements of the genomes along with surrogates are presented.
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Polychronopoulos D, Sellis D, Almirantis Y. Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics. PLoS One 2014; 9:e95437. [PMID: 24787386 PMCID: PMC4008492 DOI: 10.1371/journal.pone.0095437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 12/31/2022] Open
Abstract
Conserved, ultraconserved and other classes of constrained elements (collectively referred as CNEs here), identified by comparative genomics in a wide variety of genomes, are non-randomly distributed across chromosomes. These elements are defined using various degrees of conservation between organisms and several thresholds of minimal length. We here investigate the chromosomal distribution of CNEs by studying the statistical properties of distances between consecutive CNEs. We find widespread power-law-like distributions, i.e. linearity in double logarithmic scale, in the inter-CNE distances, a feature which is connected with fractality and self-similarity. Given that CNEs are often found to be spatially associated with genes, especially with those that regulate developmental processes, we verify by appropriate gene masking that a power-law-like pattern emerges irrespectively of whether elements found close or inside genes are excluded or not. An evolutionary model is put forward for the understanding of these findings that includes segmental or whole genome duplication events and eliminations (loss) of most of the duplicated CNEs. Simulations reproduce the main features of the observed size distributions. Power-law-like patterns in the genomic distributions of CNEs are in accordance with current knowledge about their evolutionary history in several genomes.
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Affiliation(s)
- Dimitris Polychronopoulos
- Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Athens, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Diamantis Sellis
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Yannis Almirantis
- Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Athens, Greece
- * E-mail:
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Abstract
The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non-protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.
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Cronin MA, Rincon G, Meredith RW, MacNeil MD, Islas-Trejo A, Cánovas A, Medrano JF. Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences. ACTA ACUST UNITED AC 2014; 105:312-23. [PMID: 24477675 DOI: 10.1093/jhered/est133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.
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Affiliation(s)
- Matthew A Cronin
- the School of Natural Resources and Agricultural Sciences, University of Alaska Fairbanks, Palmer Research Center, 1509 South Trunk Road, Palmer, AK 99645
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Makunin IV, Shloma VV, Stephen SJ, Pheasant M, Belyakin SN. Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One 2013; 8:e82362. [PMID: 24349264 PMCID: PMC3862641 DOI: 10.1371/journal.pone.0082362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022] Open
Abstract
Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
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Affiliation(s)
- Igor V. Makunin
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
- * E-mail:
| | - Viktor V. Shloma
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
| | - Stuart J. Stephen
- Computational Biology Group, CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Michael Pheasant
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
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Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130021. [PMID: 24218634 PMCID: PMC3826495 DOI: 10.1098/rstb.2013.0021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances. Previous studies have found that, while these regions are under strong purifying selection, and not mutational coldspots, deletion of entire regions in mice does not necessarily lead to identifiable changes in phenotype during development. These opposing findings lead to several questions regarding their functional importance and why they are under strong selection in the first place. In this perspective, we discuss the methods and techniques used in identifying and dissecting these regions, their observed patterns of conservation, and review the current hypotheses on their functional significance.
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Affiliation(s)
- Nathan Harmston
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, , Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales. Syst Biol 2013; 63:83-95. [DOI: 10.1093/sysbio/syt061] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian Tilston Smith
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Michael G. Harvey
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C. Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Travis C. Glenn
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Robb T. Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; 3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and 4Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
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40
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Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G, Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire P, Birney E, Müller F, Stupka E. Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Res 2013; 41:3600-18. [PMID: 23393190 PMCID: PMC3616699 DOI: 10.1093/nar/gkt030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 01/17/2023] Open
Abstract
Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as 'Olfactores conserved non-coding elements'.
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Affiliation(s)
- Remo Sanges
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Yavor Hadzhiev
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marion Gueroult-Bellone
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Agnes Roure
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marco Ferg
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Nicola Meola
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Gabriele Amore
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Swaraj Basu
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Euan R. Brown
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Marco De Simone
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Francesca Petrera
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Danilo Licastro
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Uwe Strähle
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Sandro Banfi
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Patrick Lemaire
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Ewan Birney
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Ferenc Müller
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
| | - Elia Stupka
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy, Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK, Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, F-13288 Marseille cedex 9, France, Centre de Recherche de Biochimie Macromoléculaire (CRBM), UMR5237 CNRS/Universités Montpellier 1, 2, 1919 route de Mende, F-34293 Montpellier cedex 5, France, Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics and University of Heidelberg, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Telethon Institute of Genetics and Medicine, 80131 Naples, Italy, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK, CBM Scrl, AREA Science Park, Basovizza, 34149 Trieste, Italy, Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy
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McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 2013; 66:526-38. [DOI: 10.1016/j.ympev.2011.12.007] [Citation(s) in RCA: 445] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/09/2023]
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Ryu T, Seridi L, Ravasi T. The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol 2012; 12:236. [PMID: 23217155 PMCID: PMC3556307 DOI: 10.1186/1471-2148-12-236] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 11/09/2012] [Indexed: 11/10/2022] Open
Abstract
Background Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors.
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Affiliation(s)
- Taewoo Ryu
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Abstract
Heart function requires sophisticated regulatory networks to orchestrate organ development, physiological responses, and environmental adaptation. Until recently, it was thought that these regulatory networks are composed solely of protein-mediated transcriptional control and signaling systems; consequently, it was thought that cardiac disease involves perturbation of these systems. However, it is becoming evident that RNA, long considered to function primarily as the platform for protein production, may in fact play a major role in most, if not all, aspects of gene regulation, especially the epigenetic processes that underpin organogenesis. These include not only well-validated classes of regulatory RNAs, such as microRNAs, but also tens of thousands of long noncoding RNAs that are differentially expressed across the entire genome of humans and other animals. Here, we review this emerging landscape, summarizing what is known about their functions and their role in cardiac biology, and provide a toolkit to assist in exploring this previously hidden layer of gene regulation that may underpin heart adaptation and complex heart diseases.
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Affiliation(s)
- Nicole Schonrock
- From the Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia (N.S., R.R.H.); St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia (N.S., R.P.H., J.S.M.); and Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia (J.S.M.)
| | - Richard P. Harvey
- From the Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia (N.S., R.R.H.); St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia (N.S., R.P.H., J.S.M.); and Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia (J.S.M.)
| | - John S. Mattick
- From the Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia (N.S., R.R.H.); St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia (N.S., R.P.H., J.S.M.); and Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia (J.S.M.)
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Kritsas K, Wuest SE, Hupalo D, Kern AD, Wicker T, Grossniklaus U. Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res 2012; 22:2455-66. [PMID: 22987666 PMCID: PMC3514675 DOI: 10.1101/gr.129346.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.
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Affiliation(s)
- Konstantinos Kritsas
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University Zürich, CH-8008 Zürich, Switzerland
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Pinheiro H, Carvalho J, Oliveira P, Ferreira D, Pinto MT, Osório H, Licastro D, Bordeira-Carriço R, Jordan P, Lazarevic D, Sanges R, Stupka E, Huntsman D, Seruca R, Oliveira C. Transcription initiation arising from E-cadherin/CDH1 intron2: a novel protein isoform that increases gastric cancer cell invasion and angiogenesis. Hum Mol Genet 2012; 21:4253-69. [PMID: 22752307 DOI: 10.1093/hmg/dds248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Disruption of E-cadherin (CDH1 gene) expression, subcellular localization or function arises during initiation and progression of almost 90% of all epithelial carcinomas. Nevertheless, the mechanisms through which this occurs are largely unknown. Previous studies showed the importance of CDH1 intron 2 sequences for proper gene and protein expression, supporting these as E-cadherin cis-modulators. Through RACE and RT-PCR, we searched for transcription events arising from CDH1 intron 2 and discovered several new transcripts. One, named CDH1a, with high expression in spleen and absent from normal stomach, was demonstrated to be translated into a novel isoform, differing from canonical E-cadherin in its N-terminal, as determined by mass spectrometry. Quantitative and functional assays showed that when overexpressed in an E-cadherin negative context, CDH1a replaced canonical protein interactions and functions. However, when co-expressed with canonical E-cadherin, CDH1a increased cell invasion and angiogenesis. Further, interferon-induced gene IFITM1 and IFI27 levels were increased upon CDH1a overexpression. Effects on invasion and IFITM1 and IFI27 expression were reverted upon CDH1a-specific knockdown. Importantly, CDH1a was de novo expressed in gastric cancer cell lines. This study presents a new mechanism by which E-cadherin functions are impaired by cis-regulatory mechanisms possibly with the involvement of inflammatory machinery. If confirmed in other cancer models, our data enclose potential for designing targeted therapies to rescue E-cadherin function.
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Affiliation(s)
- Hugo Pinheiro
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto 4200-465, Portugal
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Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms. Genetics 2012; 192:253-66. [PMID: 22714408 DOI: 10.1534/genetics.112.141945] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ultraconserved elements in the human genome likely harbor important biological functions as they are dosage sensitive and are able to direct tissue-specific expression. Because they are under purifying selection, variants in these elements may have a lower frequency in the population but a higher likelihood of association with complex traits. We tested a set of highly constrained SNPs (hcSNPs) distributed genome-wide among ultraconserved and nearly ultraconserved elements for association with seven traits related to reproductive (age at natural menopause, number of children, age at first child, and age at last child) and overall [longevity, body mass index (BMI), and height] fitness. Using up to 24,047 European-American samples from the National Heart, Lung, and Blood Institute Candidate Gene Association Resource (CARe), we observed an excess of associations with BMI and height. In an independent replication panel the most strongly associated SNPs showed an 8.4-fold enrichment of associations at the nominal level, including three variants in previously identified loci and one in a locus (DENND1A) previously shown to be associated with polycystic ovary syndrome. Finally, using 1430 family trios, we showed that the transmissions from heterozygous parents to offspring of the derived alleles of rare (frequency ≤ 0.5%) hcSNPs are not biased, particularly after adjusting for the rates of genotype missingness and error in the data. The lack of transmission bias ruled out an immediately and strongly deleterious effect due to the rare derived alleles, consistent with the observation that mice homozygous for the deletion of ultraconserved elements showed no overt phenotype. Our study also illustrated the importance of carefully modeling potential technical confounders when analyzing genotype data of rare variants.
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Lemmon AR, Emme SA, Lemmon EM. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol 2012; 61:727-44. [PMID: 22605266 DOI: 10.1093/sysbio/sys049] [Citation(s) in RCA: 558] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.
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Affiliation(s)
- Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA.
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Takahashi M, Saitou N. Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes. Genome Biol Evol 2012; 4:641-57. [PMID: 22505575 PMCID: PMC3381673 DOI: 10.1093/gbe/evs035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2012] [Indexed: 01/12/2023] Open
Abstract
Vertebrate genome comparisons revealed that there are highly conserved noncoding sequences (HCNSs) among a wide range of species and many of which contain regulatory elements. However, recently emerged sequences conserved in specific lineages have not been well studied. Toward this end, we identified 8,198 primate and 21,128 specific HCNSs as representative ones among mammals from human-marmoset and mouse-rat comparisons, respectively. Derived allele frequency analysis of primate-specific HCNSs showed that these HCNSs were under purifying selection, indicating that they may harbor important functions. We selected the top 1,000 largest HCNSs and compared the lineage-specific HCNS-flanking genes (LHF genes) with ultraconserved element (UCE)-flanking genes. Interestingly, the majority of LHF genes were different from UCE-flanking genes. This lineage-specific set of LHF genes was more enriched in protein-binding function. Conversely, the number of LHF genes that were also shared by UCEs was small but significantly larger than random expectation, and many of these genes were involved in anatomical development as transcriptional regulators, suggesting that certain groups of genes preferentially recruit new HCNSs in addition to old HCNSs that are conserved among vertebrates. This group of LHF genes might be involved in the various levels of lineage-specific evolution among vertebrates, mammals, primates, and rodents. If so, the emergence of HCNSs in and around these two groups of LHF genes developed lineage-specific characteristics. Our results provide new insight into lineage-specific evolution through interactions between HCNSs and their LHF genes.
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Affiliation(s)
- Mahoko Takahashi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Japan
- Division of Population Genetics, National Institute of Genetics, Japan
- Present address: Department of Genetics, Stanford University
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Japan
- Division of Population Genetics, National Institute of Genetics, Japan
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Abstract
Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.
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Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 2012; 61:717-26. [PMID: 22232343 DOI: 10.1093/sysbio/sys004] [Citation(s) in RCA: 667] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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Affiliation(s)
- Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.
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