Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

Dockter, Rhyan B; Elzinga, David B; Geary, Brad; Maughan, P Jeff; Johnson, Leigh A; Tumbleson, Danika; Franke, JanaLynn; Dockter, Keri; Stevens, Mikel R

doi:10.1186/1471-2156-14-66

Table 3 Summary of marker characteristics including the primary SSR motif identified in the original GR-RSC (genome reduction using restriction site conservation) sequence, primer sequences, EFL (expected fragment length), total bands, and fragment sizes

From: Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

Marker name¹	Primary motif	Forward primer (5′-3′)	GenBank accession ID	EFL	Total unique bands	Fragment size
Marker name¹	Primary motif	Reverse primer (5′-3′)	GenBank accession ID	EFL	Total unique bands	*P. cyananthus*	*P. davidsonii*	*P. dissectus*	*P. fruticosus*
PS003 ^(di,f)	(AT)₈	TGCCTCTGTCTTTACATTCCAA	JQ966997	217	3	360	260	250	260
PS003 ^(di,f)	(AT)₈	CATGAAGCACTGCAAATCCA	JQ966997	217	3	360	260	250	260
PS004 ^(da,f)	(ATT)₆	TGTTTCAATTGCTGTCCACAT	JQ951613	476	3	420	460	440	460
PS004 ^(da,f)	(ATT)₆	TTGTCTGTCCAAACGGTAGGT	JQ951613	476	3	420	460	440	460
PS005 ^(c,di,f)	(GAA)₆	GCCCAACTTCCGTAATTGAA	JQ966998	303	3	260, 300	260	280	280
		AACTGCTTGCCACTCGACTC
PS009 ^(c,da,f)	(TGA)₆	ACCTCGAACTTGACGGTCC	JQ966999	466	4	370, 650	540	650	600
		TTCTGAGGAGAAACCAAGGG
PS011 ^(da,f)	(GA)₈	AAGTGCGACACTGGATGTCTT	JQ951614	435	2	860	500	860	500
		GCAGCTTCAGCTCCAGAAAT
PS012 ^(c)	(TA)₈	TCCATATTGTAACCAACAATGACTG	JQ951615	402	3	400	360	370	360
		TGAATGGCAAACCGTAATCA
PS013 ^(f)	(TA)₈	GAAGAATTGATTTAAACAAGATGCAA	JQ967000	399	2	400	650	650	400
		TCAGTACGTGAGAAACTTGATCAATAA
PS014 ^(c)	(TGA)₆	CGATTTGGTATAGTTGGATTACGA	JQ951616	409	3	410	370	380	410
		CCTTCATCACCCGGTACTTG
PS015 ^(di)	(TCG)₆	GCCGAGTTTCAAGAAAGCAA	JQ967001	409	2	490	500	490	490
		AATTACGACCTGCCACGC
PS016 ^(c,di)	(CT)₈	CATGGCCCTTTCTTCACACT	JQ967002	447	3	NM²	1,100	1,060	1,030
		GACGCGGTTGGCTATACAGT
PS017 ^(da,di)	(AG)₉	GAAGGCTTAGCATAAATCCTCAAA	JQ951617	455	2	750	700	750	700
		ATTAGGCTCCCACGAACAAA
PS019 ^(c,di)	(AG)₈	AATCCCACAGCCCATACAAA	JQ967003	473	1	380	380	380	380
		TGAATTGAGTCCTATACCCTATTTCAA
PS021 ^(f)	(CT)₈	CTTTAGCTTAGCTGGAATACACGTT	JQ967004	386	3	350	450	450	420
		AGATTCTTGCATCACAGTTCAATTA
PS023 ^(da)	(AG)₈	GCTGGAGAATAACATGGCG	JQ967005	469	4	310	480	120, 740	480
		CCATCTTGCAAGTCCATACG
PS024 ^(da,f)	(CTG)₆	CTTCTTGCCCTGTGCCTCT	JQ967006	403	2	430	430	400	430
		CCACCACCAACAACAACAAC
PS025 ^(c,di)	(TC)₉	GCACATGAATGAAGGAATGC	JQ967007	440	3	440	410	440	400
		ACGATCTGTGAAGGAACCCA
PS026 ^(c,da,di,f)	(CTT)₆	ACTTAATAATGCCTCCTTGTGTCA	JQ967008	465	1	460	NM	460	460
		TTCCGCAACGTTGTATTTGA
PS028 ^(di)	(AC)₉	GGGAGGCAGGTAACAACAAA	JQ967009	316	4	950	400, 460	320	400, 460
		TACCTCTGCCGAACTGGATT
PS029 ^(di)	(TA)₈	ACCAAGTTGTTGGATGTTTGG	JQ967010	440	3	840	500	500	420
		GGTTTGGAATGAGACTTAGAAGGA
PS032 ^(c,di)	(GT)₉	ACAAAGTCTCCTCAATCGCC	JQ951618	328	2	370	370	370	340
		GCATGTACCGTGCACACACT
PS034 ^(c)	(AC)₉	CCAAACAAATCAAACAGCACTC	JQ951619	322	5	310, 340	320, 950	320	360
		CATGCGAATCAGTGTTGCTAA
PS035 ^(da,f)	(TC)₉	TTGCACAGCTACTTTGGCAT	JQ951620	486	3	630	520	920	520
		ATCTGTCCAAGGCATGGAAT
PS036 ^(c,di)	(TA)₈	TTCCTAATTTGGTAGCTGCAATC	JQ967011	405	3	770	770, 820	590	770
		TCCGAGGAACTATTGCCATT
PS038 ^(c,da)	(TA)₈	GTAATTACTTCGGCAGTTTGTTAATTT	JQ967012	100	1	NM	100	100	NM
		GGTGCGACCTAATTACGTTTCTAT
PS040 ^(da)	(CA)₉	TAAAGAGGCTTAAGCGCGG	JQ967013	399	3	380	390	410	390
		ACCTGAAGAGCTGCGGAGTA
PS041 ^(c,da,di,f)	(AT)₈	TTTCCGCAAGAGAAGAGCAT	JQ967014	249	3	270	670	270	240
		CTTGTGCACGATTCCATTGT
PS045 ^(c,da)	(CT)₈	GCCACATACATGAAACGTGAA	JQ967015	366	4	460	NM	440	120, 400
		CGAACTCTCTTGTGTTTCTCCC
PS047 ^(c,di,f)	(AC)₈	ACACGACATCGTTTCAGCAA	JQ967016	428	3	470, 510	440	470	470
		GCGTATGGAGAGATTTGGGA
PS048 ^(c,di)	(CA)₉	GCATTAGATGCCGAAATATCTACAA	JQ951621	436	3	420	440	380	420
		TGCCTGTAGGTTGATTTCCTTT
PS049 ^(c,da,di,f)	(AG)₈	CCCATCAATAAAGAAAGAAAGAAAGA	JQ967017	436	2	460	460	1,000	460
		GGTGAAACCCTGTCCTAAACC
PS050 ^(c,di)	(AT)₉	GTGTAACCTCTGAACAAGTTTACTGAA	JQ967018	434	2	480	460	480	460
		TGCAGTGAGCCATGCTATTC
PS051 ^(c,di,f)	(TG)₈	TGTAACACGACAATTTAACTCTTTCA	JQ967019	352	1	280	NM	280	280
		CGAGAACTCTTTCCGAGAACC
PS052 ^(c,da,di,f)	(AC)₉	CGCGGTCAATCTTGAAATCT	JQ951622	206	1	220	220	220	220
		TGACTTCCTCTCTCTCTCTCACAC
PS053 ^(di)	(AC)₈	AATCATAGTCTCGAGCGCGT	JQ951623	410	3	160, 320	320	320, 450	320
		GAGATAAATTAGATCAGCGCATCA
PS054 ^(c,da,f)	(GA)₈	TCGTTAAGCAATCTCGGAGC	JQ967020	192	3	200	200	180	190
		TCGACTGGAGAGCAAAGCA
PS055 ^(f)	(AG)₈	TGTGGTCCGGTTCCATAAAC	JQ967021	412	4	960	500	1,040	470
		TTTGTCTCCCTAATATGTGTGATGAT
PS056 ^(da,di)	(TG)₈	CATGTTTCAGGATTGGGCTT	JQ967022	319	4	690	450	230	340
		CGGTTACACACAGGTTGTTGA
PS057 ^(da,f)	(AT)₈	TGCCTAATGGACCTGATCCT	JQ967023	402	2	570	440	570	440
		CCCAATTGTTTGAAGAAAGAACA
PS058 ^(da)	(AT)₉	GTGCAACCAATGCAACTAATTC	JQ967024	469	1	NM	720	NM	720
		TCTCTCATTTCCAATGATTTCTCA
PS059 ^(di)	(CT)₈	CATCAATTGACACACAAGCAGA	JQ967025	312	2	930	340	340	340
		TCGAATCTTAAAGAAACACATCCA
PS060 ^(c,di)	(AC)₉	CCATGAGAAGTAGATGACTGGGA	JQ967026	484	2	560	560	560	540
		TTGTAATTATGATTAACTTCCCTCGTT
PS061 ^(da,f)	(TA)₈	CGACCAATCATCAACCAACA	JQ967027	453	3	480	480, 530	450, 480	NM
		GACGGGCAGAATAATTGGAA
PS062 ^(c,di)	(TA)₉	TGGAGAGGGTACGAAAGTGC	JQ967028	320	2	350	290	350	290
		CAACGATCGATTATTAGCACCA
PS064 ^(c,da,f)	(AG)₈	ATGGATGCCCTATGGGTACA	JQ967029	437	4	490	500, 680	470	470
		TGAAATGGAGGGAGTAATATAAACAA
PS066 ^(di)	(GA)₉	CAAGGATGCAGGCTCTCATT	JQ967030	434	2	250	480	250, 480	480
		CTCTGCTCGTCGTAGTGCAA
PS068 ^(c,da,di,f)	(GA)₈	TTTGGGATGCATTTCTCCAC	JQ967031	463	2	500	500	480	480
		TCAAAGTGACATCTTCCAACAAA
PS069 ^(di)	(GT)₈	CATTGGGTCAGATTTGGCTT	JQ967032	309	4	220	210	390	350
		GCTTTCAGTTTGTATATTTGTGCC
PS071 ^(c,di)	(AT)₈	AAGATGGCCCTGATCTGTTG	JQ967033	446	1	NM	NM	490	NM
		TTCGTGGGAGTTGCAAATTA
PS074 ^(c,da,di,f)	(AAG)₆	AGAAATCTCGCTCTCCACGA	JQ967034	168	1	170	170	170	170
		CGACAACCTTAGTGATCGCTTT
PS075 ^(c,da,di,f)	(TA)₈	CACCACTTTCGCAGCATTTA	JQ951624	120	2	160	140	140	140
		CAAATTACATTATTGTATGGAAACACG
PS076 ^(c,di)	(GTG)₆	CTGACAGCAACATGAACATGAA	JQ967035	161	1	170	170	170	170
		CAATCTTTGCCAATTTCCCA

¹ Parentheses indicates the species possessing sequence from which primers were designed (c = P. cyananthus, da = P. davidsonii, di = P. dissectus, f = P. fruticosus).
² NM = no marker.

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