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Article ; Online: Insights into mammalian TE diversity through the curation of 248 genome assemblies.

2023 Volume 380, Issue 6643, Page(s) eabn1430

Abstract: We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show ... ...

Abstract	We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.
MeSH term(s)	Animals ; Female ; Pregnancy ; DNA Transposable Elements ; Evolution, Molecular ; Long Interspersed Nucleotide Elements ; Eutheria/genetics ; Datasets as Topic ; Feeding Behavior ; Genetic Variation
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-04-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abn1430
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Article ; Online: Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.

Paulat, Nicole S / Storer, Jessica M / Moreno-Santillán, Diana D / Osmanski, Austin B / Sullivan, Kevin A M / Grimshaw, Jenna R / Korstian, Jennifer / Halsey, Michaela / Garcia, Carlos J / Crookshanks, Claudia / Roberts, Jaquelyn / Smit, Arian F A / Hubley, Robert / Rosen, Jeb / Teeling, Emma C / Vernes, Sonja C / Myers, Eugene / Pippel, Martin / Brown, Thomas /

Hiller, Michael / Rojas, Danny / Dávalos, Liliana M / Lindblad-Toh, Kerstin / Karlsson, Elinor K / Ray, David A

Molecular biology and evolution

2023 Volume 40, Issue 5

Abstract: Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate ... ...

Abstract	Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.
MeSH term(s)	Animals ; DNA Transposable Elements/genetics ; Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msad092
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Article: Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats

Platt, Roy N / Faircloth, Brant C / Sullivan, Kevin A M / Kieran, Troy J / Glenn, Travis C / Vandewege, Michael W / Lee, Thomas E / Baker, Robert J / Stevens, Richard D / Ray, David A / Hahn, Matthew

Systematic biology. 2018 Mar. 01, v. 67, no. 2

2018

Abstract: The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred ... ...

Abstract	The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
Keywords	Myotis ; geographical distribution ; introgression ; loci ; mammals ; mitochondria ; mitochondrial genome ; nuclear genome ; phylogeny ; topology
Language	English
Dates of publication	2018-0301
Size	p. 236-249.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syx070
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths.

Ray, David A / Grimshaw, Jenna R / Halsey, Michaela K / Korstian, Jennifer M / Osmanski, Austin B / Sullivan, Kevin A M / Wolf, Kristen A / Reddy, Harsith / Foley, Nicole / Stevens, Richard D / Knisbacher, Binyamin A / Levy, Orr / Counterman, Brian / Edelman, Nathaniel B / Mallet, James

Genome biology and evolution

2019 Volume 11, Issue 8, Page(s) 2162–2177

Abstract: Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting ... ...

Abstract	Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.
MeSH term(s)	Animals ; Butterflies/classification ; Butterflies/genetics ; DNA Transposable Elements ; Evolution, Molecular ; Gene Expression Regulation ; Genome, Insect ; Insect Proteins/genetics ; Phylogeny ; Short Interspersed Nucleotide Elements
Chemical Substances	DNA Transposable Elements ; Insect Proteins
Language	English
Publishing date	2019-08-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evz125
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Article ; Online: (with research data) Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

Platt, Roy N / Faircloth, Brant C / Sullivan, Kevin A M / Kieran, Troy J / Glenn, Travis C / Vandewege, Michael W / Lee, Thomas E / Baker, Robert J / Stevens, Richard D / Ray, David A

Systematic biology

2017 Volume 67, Issue 2, Page(s) 236–249

Abstract	The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
MeSH term(s)	Animals ; Chiroptera/classification ; Chiroptera/genetics ; Genome/genetics ; Genome, Mitochondrial/genetics ; Phylogeny
Language	English
Publishing date	2017-09-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syx070
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Article ; Online: Six reference-quality genomes reveal evolution of bat adaptations.

Jebb, David / Huang, Zixia / Pippel, Martin / Hughes, Graham M / Lavrichenko, Ksenia / Devanna, Paolo / Winkler, Sylke / Jermiin, Lars S / Skirmuntt, Emilia C / Katzourakis, Aris / Burkitt-Gray, Lucy / Ray, David A / Sullivan, Kevin A M / Roscito, Juliana G / Kirilenko, Bogdan M / Dávalos, Liliana M / Corthals, Angelique P / Power, Megan L / Jones, Gareth /

Ransome, Roger D / Dechmann, Dina K N / Locatelli, Andrea G / Puechmaille, Sébastien J / Fedrigo, Olivier / Jarvis, Erich D / Hiller, Michael / Vernes, Sonja C / Myers, Eugene W / Teeling, Emma C

Nature

2020 Volume 583, Issue 7817, Page(s) 578–584

Abstract: Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing ...

Abstract	Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols
MeSH term(s)	Adaptation, Physiological/genetics ; Adaptation, Physiological/immunology ; Animals ; Chiroptera/classification ; Chiroptera/genetics ; Chiroptera/immunology ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Genome/genetics ; Genomics/standards ; Immunity/genetics ; Molecular Sequence Annotation/standards ; Phylogeny ; RNA, Untranslated/genetics ; Reference Standards ; Reproducibility of Results ; Virus Integration/genetics ; Viruses/genetics
Chemical Substances	DNA Transposable Elements ; RNA, Untranslated
Keywords	covid19
Language	English
Publishing date	2020-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2486-3
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Article ; Online: Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Wirthlin, Morgan E / Schmid, Tobias A / Elie, Julie E / Zhang, Xiaomeng / Kowalczyk, Amanda / Redlich, Ruby / Shvareva, Varvara A / Rakuljic, Ashley / Ji, Maria B / Bhat, Ninad S / Kaplow, Irene M / Schäffer, Daniel E / Lawler, Alyssa J / Wang, Andrew Z / Phan, BaDoi N / Annaldasula, Siddharth / Brown, Ashley R / Lu, Tianyu / Lim, Byung Kook /

Azim, Eiman / Clark, Nathan L / Meyer, Wynn K / Pond, Sergei L Kosakovsky / Chikina, Maria / Yartsev, Michael M / Pfenning, Andreas R / Andrews, Gregory / Armstrong, Joel C / Bianchi, Matteo / Birren, Bruce W / Bredemeyer, Kevin R / Breit, Ana M / Christmas, Matthew J / Clawson, Hiram / Damas, Joana / Di Palma, Federica / Diekhans, Mark / Dong, Michael X / Eizirik, Eduardo / Fan, Kaili / Fanter, Cornelia / Foley, Nicole M / Forsberg-Nilsson, Karin / Garcia, Carlos J / Gatesy, John / Gazal, Steven / Genereux, Diane P / Goodman, Linda / Grimshaw, Jenna / Halsey, Michaela K / Harris, Andrew J / Hickey, Glenn / Hiller, Michael / Hindle, Allyson G / Hubley, Robert M / Hughes, Graham M / Johnson, Jeremy / Juan, David / Karlsson, Elinor K / Keough, Kathleen C / Kirilenko, Bogdan / Koepfli, Klaus-Peter / Korstian, Jennifer M / Kozyrev, Sergey V / Lawless, Colleen / Lehmann, Thomas / Levesque, Danielle L / Lewin, Harris A / Li, Xue / Lind, Abigail / Lindblad-Toh, Kerstin / Mackay-Smith, Ava / Marinescu, Voichita D / Marques-Bonet, Tomas / Mason, Victor C / Meadows, Jennifer R S / Moore, Jill E / Moreira, Lucas R / Moreno-Santillan, Diana D / Morrill, Kathleen M / Muntané, Gerard / Murphy, William J / Navarro, Arcadi / Nweeia, Martin / Ortmann, Sylvia / Osmanski, Austin / Paten, Benedict / Paulat, Nicole S / Pollard, Katherine S / Pratt, Henry E / Ray, David A / Reilly, Steven K / Rosen, Jeb R / Ruf, Irina / Ryan, Louise / Ryder, Oliver A / Sabeti, Pardis C / Serres, Aitor / Shapiro, Beth / Smit, Arian F A / Springer, Mark / Srinivasan, Chaitanya / Steiner, Cynthia / Storer, Jessica M / Sullivan, Kevin A M / Sullivan, Patrick F / Sundström, Elisabeth / Supple, Megan A / Swofford, Ross / Talbot, Joy-El / Teeling, Emma / Turner-Maier, Jason / Valenzuela, Alejandro / Wagner, Franziska / Wallerman, Ola / Wang, Chao / Wang, Juehan / Weng, Zhiping / Wilder, Aryn P / Xue, James R

Science (New York, N.Y.)

2024 Volume 383, Issue 6690, Page(s) eabn3263

Abstract: Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian ... ...

Abstract	Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (
MeSH term(s)	Animals ; Chiroptera/genetics ; Chiroptera/physiology ; Vocalization, Animal/physiology ; Motor Cortex/cytology ; Motor Cortex/physiology ; Chromatin/metabolism ; Enhancer Elements, Genetic ; Motor Neurons/physiology ; Larynx/physiology ; Epigenesis, Genetic ; Genome ; Gene Expression Regulation ; Evolution, Molecular ; Proteins/genetics ; Proteins/metabolism ; Amino Acid Sequence ; Eutheria/genetics ; Eutheria/physiology ; Machine Learning
Chemical Substances	Chromatin ; Proteins
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abn3263
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Zs.MG 77: Show issues

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Article: Six reference-quality genomes reveal evolution of bat adaptations

Jebb, David / Huang, Zixia / Pippel, Martin / Hughes, Graham M. / Lavrichenko, Ksenia / Devanna, Paolo / Winkler, Sylke / Jermiin, Lars S. / Skirmuntt, Emilia C. / Katzourakis, Aris / Burkitt-Gray, Lucy / Ray, David A. / Sullivan, Kevin A. M. / Roscito, Juliana G. / Kirilenko, Bogdan M. / Dávalos, Liliana M. / Corthals, Angelique P. / Power, Megan L. / Jones, Gareth /

Ransome, Roger D. / Dechmann, Dina K. N. / Locatelli, Andrea G. / Puechmaille, Sébastien J. / Fedrigo, Olivier / Jarvis, Erich D. / Hiller, Michael / Vernes, Sonja C. / Myers, Eugene W. / Teeling, Emma C.

Nature

Abstract: Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity High-quality genomes are crucial for understanding the molecular basis and evolution of these traits Here we incorporated long-read sequencing ... ...

Abstract	Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity High-quality genomes are crucial for understanding the molecular basis and evolution of these traits Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus) We integrated gene projections from our 'Tool to infer Orthologs from Genome Alignments' (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade We found selection and loss of immunity-related genes (including pro-inflammatory NF-kB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #826613
Database	COVID19

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Article ; Online: Insights into mammalian TE diversity through the curation of 248 genome assemblies.

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Article ; Online: Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.

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Article: Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats

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Article ; Online: Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths.

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Article ; Online: (with research data) Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

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Article ; Online: Six reference-quality genomes reveal evolution of bat adaptations.

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Article ; Online: Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

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Article: Six reference-quality genomes reveal evolution of bat adaptations

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