Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae)

Farkašová, Helena; Hron, Tomáš; Pačes, Jan; Hulva, Pavel; Benda, Petr; Gifford, Robert J.; Elleder, Daniel

doi:10.1073/pnas.1621224114

Cited by 32 publications

(39 citation statements)

References 35 publications

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“…We also detected pol sequences in the Molossus genome clustering closely with reference delta sequences (Bovine Leukemia virus – BLV, Human T-lymphotropic Virus – HTLV). Pol regions for delta retroviruses in bats have not been detected before, with only partial gag and a single LTR identified previously in Miniopterus and Rhinolophus species 94,98 .…”

Section: Introductionmentioning

confidence: 79%

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

Jebb

Huang

Pippel

et al. 2019

Preprint

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42 43 ^Joint first authors 44 *joint senior/corresponding authors emails 45 Michael Hiller: hiller@mpi-cbg.de 46 Sonja Vernes: sonja.vernes@mpi.nl 47 Eugene Myers: gene@mpi-cbg.de 48 Emma C. Teeling: emma.teeling@ucd.ie 49 2 Abstract: Bats account for ~20% of all extant mammal species and are considered exceptional 50given their extraordinary adaptations, including biosonar, true flight, extreme longevity, and 51 unparalleled immune systems. To understand these adaptations, we generated reference-quality 52 genomes of six species representing the key divergent lineages. We assembled these genomes 53 with a novel pipeline incorporating state-of-the-art long-read and long-range sequencing and 54 assembly techniques. The genomes were annotated using a maximal evidence approach, de 55 novo predictions, protein/mRNA alignments, Iso-seq long read and RNA-seq short read 56 transcripts, and gene projections from our new TOGA pipeline, retrieving virtually all (>99%) 57 mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 58 conserved non-coding elements identified across 48 mammalian genomes helped to resolve 59 bats' closest extant relatives within Laurasiatheria, supporting a basal position for bats within 60 Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on 61 hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal 62 echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and 63 loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB 64 signalling; and (c) expansion of the APOBEC family, associated with restricting viral infection, 65 transposon activity and interferon signalling. We also identified unique integrated viruses, 66 indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. 67Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory 68 relationships that may contribute to phenotypic diversity in bats. Together, our reference-69 quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed 70 previously unknown genomic adaptations in bats that may explain their extraordinary traits. 71 72

show abstract

Section: Introductionmentioning

confidence: 79%

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

Jebb

Huang

Pippel

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Åãî íàçâàëè MINERVa (Miniopterus endogenous retrovirus) è îí ÿâëÿåòñÿ ýíäîãåííûì ðåòðîâèðóñîì (endogenous retroviruse -ERV) äëèííîêðûëûõ ëåòó÷èõ ìûøåé (âèäû ðîäà Miniopterus ñåìåéñòâà Miniopteridae). Ýòà íàõîäêà ðàñøèðÿåò ãðàíèöû ðàñïðîñòðàíåíèÿ äåëüòàðåòðîâèðóñîâ ñðåäè ðàçëè÷íûõ âèäîâ aeèâîòíûõ [10,18].…”

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“…Îòëè÷èòåëüíîé ñòðóêòóðíîé ÷åðòîé äåëüòàðåòðîâèðóñîâ ÿâëÿåòñÿ íàëè÷èå â ñîñòàâå èõ ïðîâèðóñíîé ÄÍÊ, êðîìå îáùèõ äëÿ âñåõ ðåòðîâèðóñîâ ãåíîâ 5′-gag-pro-pol-env-3′, êîäèðóþùèõ áåëêè âèðèîíà, ðåãóëÿòîðíûõ ãåíîâ tax è rex [13,16,20,31]. Äëÿ MINERVa áûëî òàêaeå ïðåäïîëîaeåíî íàëè-÷èå îðòîëîãîâ tax è rex [10].…”

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“…Íàäåaeíîñòü ôèëîãåíåòè÷åñêèõ îòíîøåíèé îöåíèâàëàñü ñ ïîìîùüþ íåïàðàìåòðè÷åñêîãî áóòñòðýï-àíàëèçà ñ èñïîëüçîâàíèåì 1000 ïîâòîðíîñòåé [11]. Îòêðûòàÿ ðàìêà òðàíñëÿöèè 1 (ÎÐÒ1) MINERVa, êîòîðàÿ ïðåäïîëàãàåòñÿ íà ðîëü îðòîëîãà Tax, âûâåäåíà äëÿ êàaeäîé èç ïÿòè íóêëåîòèäíûõ ïîñëåäîâàòåëüíîñòåé MINERVa (GenBank:KY250075-KY250079) ñ èñïîëüçîâàíèåì ïðîãðàììû GeneRunner è ñðàâíåíèåì ñ îïóáëèêîâàííîé ïîñëåäîâàòåëüíîñòüþ ÎÐÒ1 [10]. Äëÿ KY250077 ÎÐÒ1 íå áûëà èñïîëüçîâàíà, ò.ê.…”

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“…Ïðèìåð ãðóïïû PTLV òàêaeå ïîêàçûâàåò, ÷òî ôè-ëîãåíåòè÷åñêèå èññëåäîâàíèÿ Tax ìîãóò áûòü èñïîëüçîâàíû â êà÷åñòâå äîïîëíèòåëüíûõ ê òàêîâûì, ïðîâîäèìûì ïî ãåíàì pol, env è ïîëíîðàçìåðíûì ïðîâèðóñíûì ãåíîìàì äëÿ âíóòðèâèäîâîé êëàññèôèêàöèè. Journal "Veterinaria i kormlenie" Ïðîâåäåííûé íàìè ôèëîãåíåòè÷åñêèé àíàëèç ïîêàçàë òàêaeå, ÷òî ÎÐÒ1 MINERVà (ðèñ.1), íåñìîòðÿ íà òî, ÷òî àâòîðû [10] íå îáíàðóaeèëè êàêîé-ëèáî ñóùåñòâåííîé ãîìîëîãèè ñ ãåíîì tax, âõîäèò â îäíó ôèëîãåíåòè÷åñêóþ ãðóïïó ñ Tax BLV, õîòÿ è îòäåëüíîé âåòâüþ. Ýòî ñâèäåòåëüñòâóåò î ðàñïðîñòðàíåíèè äåëüòàðåòðîâèðóñîâ ñðåäè äàëüíåðîäñòâåííûõ âèäîâ-õîçÿåâ, à òàêaeå ïîääåðaeèâàåò ïðåäïîëîaeåíèå î òîì, ÷òî èõ ýâîëþöèîíèðîâàíèå ïðîèñõîäèò ïðè ó÷àñòèè ERVs ëåòó÷èõ ìûøåé, ÷òî ÿâëÿåòñÿ ðàñïðîñòðàíåííûì ñðåäè ðåòðîâèðóñîâ, íî íå áûëî èçâåñòíî äëÿ äåëüòàðåòðîâèðóñîâ äî îáíàðóaeåíèÿ MINERVà [14,17].…”

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