Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

Paulat, Nicole S.; Storer, Jessica M.; Moreno-Santillán, Diana D.; Osmanski, Austin; Sullivan, Kevin A.; Grimshaw, Jenna; Korstian, Jennifer M.; Halsey, Michaela K.; Garcia, Carlos J.; Crookshanks, Claudia; Roberts, Jaquelyn; Smit, Arian F. A.; Hubley, Robert; Rosen, Jeb; Teeling, Emma C.; Vernes, Sonja C.; Myers, Eugene W.; Pippel, Martin; Brown, Thomas A.; Hiller, Michael; Rojas, Danny; Dávalos, Liliana M.; Lindblad‐Toh, Kerstin; Karlsson, Elinor K.; Ray, David A.

doi:10.1101/2023.03.23.533946

Cited by 3 publications

(2 citation statements)

References 105 publications

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“…For example, long interspersed nuclear elements (LINEs) are common in aardvarks and long terminal repeat (LTR) retrotransposons have accumulated in some rodents. Bats are a hotspot for horizontal transfer of DNA transposons (detailed in 31 ), having experienced over 200 such events, whereas only 11 transposons horizontally transferred into other lineages( Table S4 ).…”

Section: Main Textmentioning

confidence: 99%

Evolutionary constraint and innovation across hundreds of placental mammals

Christmas¹,

Kaplow²,

Genereux³

et al. 2023

Preprint

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Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number and reliance on human-referenced alignments. We explore the evolution of placental mammals, including humans, through reference-free whole-genome alignment of 240 species and protein-coding alignments for 428 species. We estimate 10.7% of the human genome is evolutionarily constrained. We resolve constraint to single nucleotides, pinpointing functional positions, and refine and expand by over seven-fold the catalog of ultraconserved elements. Overall, 48.5% of constrained bases are as yet unannotated, suggesting yet-to-be-discovered functional importance. Using species-level phenotypes and an updated phylogeny, we associate coding and regulatory variation with olfaction and hibernation. Focusing on biodiversity conservation, we identify genomic metrics that predict species at risk of extinction.

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Section: Main Textmentioning

confidence: 99%

Evolutionary constraint and innovation across hundreds of placental mammals

Christmas¹,

Kaplow²,

Genereux³

et al. 2023

Preprint

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show abstract

“…We suggest tick genomes, with their close associations to the DNA of other organisms, may be a key horizontal transfer point for TEs. There is evidence that horizontal transfer of TEs can occur from eukaryote parasites to their hosts and viruses to eukaryotes [57][58][59][60][61] . For example the LINE BovB was likely horizontally transferred to different vertebrates via a tick 62 .…”

Section: Discussionmentioning

confidence: 99%

The repetitive genome of theIxodes ricinustick reveals transposable elements have driven genome evolution in ticks

Ronai,

de Paula Baptista,

Paulat

et al. 2024

Preprint

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Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tickIxodes ricinusis the key vector of Lyme borreliosis and tick-borne encephalitis in Western Eurasia.Ixodesticks have large and repetitive genomes that are not yet well characterized. Here we generate two high-qualityI.ricinusgenome assemblies, with haploid genome sizes of approximately 2.15 Gbp. We find transposable elements comprise at least 69% of the twoI.ricinusgenomes, amongst the highest proportions found in animals. The transposable elements in ticks are highly diverse and novel, so we constructed a repeat library for ticks using ourI.ricinusgenomes and the genome ofI.scapularis, another major tick vector of Lyme borreliosis. To understand the impact of transposable elements on tick genomes we compared their accumulation in the twoIxodessister species. We find transposable elements in these two species to be drivers of genome evolution in ticks. TheI.ricinusgenome assemblies and our tick repeat library will be valuable resources for biological insights into this important ectoparasite. Our findings highlight that further research into the impact of transposable elements on the genomes of blood-feeding parasites is required.

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Evolutionary constraint and innovation across hundreds of placental mammals

Christmas

Kaplow

Genereux

et al. 2023

Science

Self Cite

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Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth’s vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

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Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

Cited by 3 publications

References 105 publications

Evolutionary constraint and innovation across hundreds of placental mammals

Evolutionary constraint and innovation across hundreds of placental mammals

The repetitive genome of theIxodes ricinustick reveals transposable elements have driven genome evolution in ticks

Evolutionary constraint and innovation across hundreds of placental mammals

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