Peculiar Evolutionary History of miR390-Guided TAS3-Like Genes in Land Plants

Table 1

Description of sequenced TAS3-like loci in mosses.

Class/subclass	Order	Species	^aClone/cluster	^bLength,; bp	^cReference and/or accession number	^dOrganization; (one- or two-tasiARF/AP2/TAS6)
Bryopsida/Dicranidae	Pottiales	Bryoerythrophyllum inaequalifolium	27-Bin/; TAS3b,c,e	236	KC812740	tasiARF/AP2
	Gremiales	Coscinodon humilis	20-Chu/; TAS3b,c,e	234	Krasnikova et al., 2011 [24]; HQ709423	—“—
		C. humilis	16-Chu/; TAS3b,c,e	228	Krasnikova et al., 2011 [24]; HQ709422	—“—
		Schistidium elegantulum	24-Sce/; TAS3b,c,e	229	Krasnikova et al., 2011 [24]; HQ709424	—“—
		Grimmia cribrosa	43-Gcr/; TAS3b,c,e	228	Krasnikova et al., 2011 [24]; HQ709421	—“—
	Dicranales	Fissidens taxifolius	17-Fit/; TAS3b,c,e	192	Krasnikova et al., 2011 [24]; HQ709425	—“—
		Ceratodon purpureus	48-Cpu/; TAS3b,c,e	231; 779^e	SRR074890.1165977.2	tasiARF/AP2/; TAS6
		Amphidium mougeotii	56-Amo/; TAS3b,c,e	234	KC812745	tasiARF/AP2
		Leucobryum glaucum	41-Lgl/; TAS3b,c,e	226	KC812750	—“—
		L. glaucum	42-Lgl/; TAS3b,c,e	192	KC812749	—“—
		Dicranum pacificum	44-Dpa/; TAS3b,c,e	232	KC812741	—“—
Bryopsida/Bryidae	Orthotrichales	Orthotrichum pumilum	5-Opu/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; HQ709419	—“—
		O. pumilum	24-Opu/; TAS3a,d,f	246	Krasnikova et al., 2011 [24]; HQ709420	—“—
	Hypnales	Brachythecium latifolium	47-Br/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; FJ804748	—“—
		B. latifolium	50-Br/; TAS3a,d,f	255	Krasnikova et al., 2011 [24]; FJ804747	—“—
		B. albicans	37-Bal/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; HQ709414	—“—
		B. rivulare	11-Brar/; TAS3b,c,e	199	KC812739	—“—
		B. rivulare	36-Brar/; TAS3a,d,f	255; 1444^e	KC812738; (Illumina sequence)	tasiARF/AP2/; TAS6
		Homalothecium philippeanum	7-Hp/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; HQ709415	tasiARF/AP2
		Amblystegium sp	52-Ambly/; TAS3b,c,e	191	KC812762	—“—
		Oxyrrhynchium hians	25-Oxy/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; HQ709418	—“—
		O. hians	32-Oxy/; TAS3a,d,f	253	KC812761	—“—
		Pylaisia polyantha	10-Pyp/; TAS3b,c,e	199	Krasnikova et al., 2011 [24]; HQ709416	—“—
		P. polyantha	11-Pyp/; TAS3a,d,f	253	Krasnikova et al., 2011 [24]; HQ709417	—“—
	Hookeriales	Hookeria lucens	49-H/; TAS3b,c,e	190	Krasnikova et al., 2011 [24]; FJ804749	—“—
	Bryales	Pohlia nutans	Pnu-30698; TAS3a,d,f	259; 920^e	GACA01023180.1	tasiARF/AP2/; TAS6
		Plagiomnium medium	41-Pme/; TAS3a,d,f	236	KC812756	tasiARF/AP2
		Ptychostomum pseudotriquetrum	72-Pps/; TAS3a,d,f	246	KC812758	—“—
		P. pseudotriquetrum	16-Pps/; TAS3b,c,e	193	KC812757	—“—
		Bryum argenteum	9-Bar/; TAS3a,d,f	233	KC812760	—“—
		B. argenteum	4-Bar/; TAS3b,c,e	192	KC812759	—“—
	Bartramiales	Bartramia halleriana	32-Bha/; TAS3b,c,e	228	KC812748	—“—
		B. halleriana	28-Bha/; TAS3a,d,f	272	KC812747	—“—
		B. halleriana	29-Bha/; TAS3a,d,f	254	KC812746	—“—
Bryopsida/Funariidae	Encalyptales	Encalypta rhaptocarpa	35-Erh/; TAS3a,d,f	253	KC791767	—“—
		E. rhaptocarpa	16-Erh/; TAS3b,c,e	249	KC791768	—“—
		E. rhaptocarpa	31-Erh/; TAS3a,d,f	253	KC791769	—“—
	Funariales	Physcomitrella patens	PpTAS3a/; TAS3a,d,f	255; 895^e	Arif et al., 2012 [20]	tasiARF/AP2/; TAS6
		P. patens	PpTAS3d/; TAS3a,d,f	256; 1250^e	Arif et al., 2012 [20]	—“—
		P. patens	PpTAS3f/; TAS3a,d,f	245; 1234^e	Arif et al., 2012 [20]	—“—
		P. patens	PpTAS3c/; TAS3b,c,e	259	Arif et al., 2012 [20]	tasiARF/AP2
		P. patens	PpTAS3b/; TAS3b,c,e	192	Arif et al., 2012 [20]	—“—
		P. patens	PpTAS3e/; TAS3b,c,e	192	Arif et al., 2012 [20]	—“—
Bryopsida/Timmiidae	Timmiales	Timmia austriaca	9-Tau/; TAS3a,d,f	254	KC812755	—“—
Tetraphidopsida	Tetraphidales	Tetraphis pellucida	73-Tpe/; TAS3b,c,e	275	KC812754	—“—
		T. pellucida	80-Tpe/; outside	251	KC812753	—“—
Polytrichopsida	Polytrichales	Polytrichum commune	122-Pco/; outside	227	KC812751	—“—
		P. commune	124-Pco/; TAS3b,c,e	262	KC812752	—“—
Andreaeopsida	Andreaeales	Andreaea rupestris	13-Aru/; outside	254	KC812744	—“—
		A. rupestris	14-Aru/; outside	272	KC812743	—“—
Sphagnopsida	Sphagnales	Sphagnum squarrosum	Not found	—	Krasnikova et al., 2011 [24]	—
		S. girgensohnii	Not found	—	Krasnikova et al., 2011 [24]	—
Marchantiopsida	Marchantiales	Marchantia polymorpha	1-Mpo/; outside	256	KC812742; SRR072168.997878.2	tasiAP2

aThis column includes the names of all identified TAS3 clones (upper line) and clusterization with Physcomitrella patens loci on the dendrogram (lower line).
^bThis column indicates the length of all TAS3 species including both 5′ and 3′ miR390 target sequences on the borders.
^cThis column includes the references and accession numbers (if known) for all identified TAS3 loci except Physcomitrella patens loci. For loci 48-Cpu and 1-Mpo, our sequence data are identical to the fragments of longer sequences found in NCBI SRA database. For 36-Brar, PCR-based sequence corresponds to the fragments of the longer Illumina reads of B. rivulare genomic DNA (Goryunov et al. unpublished).
^dThis column indicates internal organization of TAS3 loci which include tasiARF and tasiAP2 sequences. TAS6 means the occurrence of the particular TAS3 locus in close proximity to TAS6 locus (if known).
^eThis number indicates total length of TAS6-TAS3 complex element (from the 5′ miR529 target site in TAS6 to 3′ miR390 target site in TAS3).