Vi­ral Abun­dance and Di­ver­sity

Pic­tures Con­sid­ered #33

by Elio

This pic­ture should hang as a poster in every mi­cro­bio­lo­gi­cal lab that is con­cerned with vi­ruses (and which one isn't, one way or an­other?). It shows how di­verse the vi­ruses that af­fect hosts of the three do­mains of life ac­tu­al­ly are, both in mor­phol­ogy and repli­ca­tion strat­egy ‒ the nu­cleic acid type of their ge­netic ma­te­r­ial is in­di­cated in the fig­ure but their repli­ca­tion strate­gies are even more di­verse. I con­fess, this is some­thing I had not fully ap­pre­ci­a­ted.

To quote the au­thors of the pa­per (Nasir, Forterre, Kim, and Cae­tano-Ar­rol­lés): "The dis­tri­b­u­tion of the as­so­ci­a­tion of vi­ral repli­con types with cells is ex­tremely bi­ased. For ex­am­ple, RNA viruses are com­ple­te­ly ab­sent in Ar­chaea and are rare in Bac­te­ria. In com­pa­ri­son, ver­te­brates host nu­mer­ous RNA and retro­viruses. Sur­pris­ingly, ds­DNA viruses are rare in plants while dsRNA viruses are abun­dant in fungi. Sim­i­larly, retro­viruses are in­te­grated into the ge­nomes of mul­ti­cel­lu­lar eu­kary­otes but are com­pletely ab­sent in the mi­cro­bial genomes. In other words, spe­cific re­la­tion­ships ex­ist be­tween the type of vi­ral repli­con and the host range."

If va­ri­ety is the spice of life, then, by this cri­te­rion, viruses are very much alive.

 

Leg­end to Fig­ures
The abun­dance and di­ver­sity of vi­ral lin­eages in the do­mains of life. A Pie-charts de­scribe the abun­dance of ds­DNA, ss­DNA, dsRNA, ss­RNA(+), ss­RNA(−), and retro­tran­scrib­ing viruses in Ar­chaea, Bac­te­ria, and Eu­karya, and within the ma­jor eu­karyal di­vi­sions. Genome data from 3660 com­pletely se­quenced vi­ral genomes cor­re­spond­ing to 1671 ds­DNA, 610 ss­DNA, 883 ss­RNA(+), 179 ss­RNA(−), 190 dsRNA, and 127 retro­tran­scrib­ing viruses were re­trieved from the Vi­ral Genomes Re­source (April, 2014). Ad­di­tion­ally, two ss­DNA ar­chaeal viruses were iden­ti­fied from the lit­er­a­ture (Pietilä et al., 2009; Mochizuki et al., 2012). Viruses that were unas­signed to any or­der, ge­ne­ra, or species and un­clas­si­fied viruses were ex­cluded from sam­pling. Viruses were broadly clas­si­fied ac­cor­ding to host pref­er­ences into the fol­low­ing cat­e­gories: Ar­chaea, Bac­te­ria, Pro­tista (an­i­mal-like pro­tists and brown al­gae), In­ver­te­brates and plants (IP); Fungi (all fungi and fungi-like pro­tists); Plants (all plants, green al­gae, and di­atoms), and Meta­zoa (ver­te­brates, in­ver­te­brates, and hu­man). Host in­for­ma­tion was avail­able for roughly 99% (3633) of the sam­pled viruses. Pie-charts are pro­por­tional to the size of each dis­tri­b­u­tion.

B Virion mor­pho­types that are spe­cific to a do­main or are shared be­tween do­mains are dis­played. Virion pic­tures were bor­rowed from the Vi­ral­Zone web-re­source (Hulo et al., 2011) and from Pietilä et al. (2014) and Pina et al. (2011). A key­word based search was per­formed on text data to as­sign the most gen­eral mor­pho­types (e.g., rod-shaped, spher­i­cal, droplet-shaped, etc) to all viruses. More than one viri­dae with same mor­pho­type is pos­si­ble but not made ex­plicit. The di­a­gram does not al­ways im­ply evo­lu­ti­o­na­ry re­la­tion­ship be­tween vi­rus­es har­bor­ing com­mon morpho­logy. For ex­am­ple, ar­chaeal and eu­karyal rod-shaped viruses are prob­a­bly not evo­lu­ti­o­na­ry re­lated (Goulet et al., 2009). Well-stud­ied ex­cep­tions are head-tail cau­dovi­rales har­bor­ing the HK97 cap­sid fold and of poly­he­dral viruses har­bor­ing the dou­ble jelly roll fold (Abres­cia et al., 2012). 1Gut­taviri­dae; 2Am­pul­la­vi­ri­dae; 3Spi­raviri­dae [name pend­ing ap­proval by ICTV]; 4Fuselloviri­dae; 5As­coviri­dae; 6Ni­maviri­dae; 7Ge­mi­ni­vi­ri­dae; 8As­tro­viri­dae; 9Rhab­doviri­dae; 10Ophio­viridae; 11Polyd­naviri­dae; (left to right) 12Rudi­viri­dae (Ar­chaea); Vir­ga­viridae (Eu­karya); 13Clavaviri­dae (Ar­chaea) Roniviri­dae (Eu­karya); 14Siphoviri­dae, My­oviri­dae, and Podo­vi­ri­dae (Ar­chaea and Bac­te­ria); 15Mi­croviri­dae (Bac­te­ria), Cir­coviri­dae (Eu­karya); 16Cys­toviri­dae (Bac­te­ria), Reo­vi­ri­dae (Eu­karya); 17Lipothrix­iviri­dae (Ar­chaea), In­oviri­dae (Bac­te­ria), Po­tyviri­dae (Eu­karya); 18Sul­folobus tur­reted icosa­he­dral virus (Ar­chaea), Tec­tiviri­dae (Bac­te­ria), Ade­n­oviri­dae (Eu­karya). Source

 

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