Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Straub, Shannon CK; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

doi:10.1186/1471-2164-12-211

Table 3 Primers designed from Asclepias syriaca microreads hitting COSII alignments

From: Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Primer Set Name	Orientation	Primer Sequence (5'-3')	Annealing Temp. (°C)
At1g24360a	FORWARD	GCAAGATCATCAAAGGAGGCA	59.0
	REVERSE	GATTTAGATCAATAACCTCCTGCCA
At1g24360b	FORWARD	GGAGGTTATTGATCTAAATCTCAC	56.3
	REVERSE	AACAAGGCCAACAACTGATG
At1g24360c	FORWARD	CAATTACAGTGCTGCAAAAGCTG	60.0
	REVERSE	CATATCAGATGCAATGAATCCGGG
At1g44760a	FORWARD	TACTCATGTTACTAATAAGGGTGA	-
	REVERSE	CTTTGCTTTGCTTCCTCACTC
At1g55880a	FORWARD	ATGTACACAAAAGAGGAGGCTG	54.0
	REVERSE	GATGCCTCATCCCACTATCAC
At1g77370a	FORWARD	CCAAAGCGCCATCTACTCCA	60.0
	REVERSE	GGCCAACCAAATCCAGAAGAAT
At2g03120a	FORWARD	GAAGGTAGATCCAAATTTGAATGTC	58.0
	REVERSE	GCAAGTCAACACAGCATTAAC
At2g06530a	FORWARD	GTGAAGGTAATGGCCAAAGATC	58.0
	REVERSE	GTAACACCTTTCATTGCTTCTCC
At2g21960a	FORWARD	ATTGGGGTTTCTTTGTTCCATAC	53.0
	REVERSE	GCAGATTGGCCAACAACTTTG
At2g21960b	FORWARD	GTTGTTGGCCAATCTGCAGA	59.0
	REVERSE	TTTGTTGCTGATCTTTGCTAAGC
At2g30200a	FORWARD	ACAAGCTGTTGGAATGGGTG	55.0
	REVERSE	ATCTCAACTGCAGCTAAGCTG
At2g30200b	FORWARD	ATCTATGTCACCAGCTTAGCTG	58.3
	REVERSE	TTTGAATGATTTTGCCTTTGCTTC
At2g30200c	FORWARD	CAAAGGCAAAATCATTCAAAGC	56.3
	REVERSE	TGCATCAACATTTGATATTACTGG
At2g34620a	FORWARD	TTCAGAAAGGTCATCAACAAATG	57.8
	REVERSE	GCTGAAAGTGAACAAACCTGG
At2g34620b	FORWARD	TGCCAACATTTCTTTACAATTCAAG	52.0
	REVERSE	none
At2g47390a	FORWARD	GTCTTGGTACAAAACACGCAAG	59.0
	REVERSE	TCAGTTTTAGATTCTTTAGAGGTAAG
At2g47390b	FORWARD	CTAATGAGTTTGCTGGCATTGG	-
	REVERSE	CACCATGTCCTTTGAGTGCG
At4g13430a	FORWARD	GAGCAAAACATAAAGTACTTCTA	48.0
	REVERSE	CATTTCACCATCCATAACAA
At4g13430b	FORWARD	GTGCCTCCAACATTGAGATTTG	59.0
	REVERSE	CATTCTCTAGCCAAAGCACGA
At4g13430c	FORWARD	GTGCTTTGGCTAGAGAATGCA	60.0
	REVERSE	CAAGACAAGCACCACAACTAGG
At4g26750a	FORWARD	GCCTGATGACCATTTACATCTTG	-
	REVERSE	TACAGGTCTCCTCCCTTCTTTC
At5g13420a	FORWARD	TGGTATGACAACCTGTGCCG	55.0
	REVERSE	GTATCATCAGCAAGTCTTGGTGAA
At5g13420b	FORWARD	CTCCATGCGTCCCTTCAATC	60.5
	REVERSE	TGGCACCTTTCTTCACCAGAG
At5g23540a	FORWARD	GTGTTGAAGCGGTTGATCATG	-
	REVERSE	TCCATCTGTCCATTTTTTCTTATGA
At5g23540b	FORWARD	none	52.0
	REVERSE	AAGGCATCAATTACCACTTTCC
At5g49970a	FORWARD	GTAGCTGCTCGTCATTTATATC	55.8
	REVERSE	GAGAATCCAAACATTGCATCA
At5g49970b	FORWARD	TTGATGCAATGTTTGGATTCTC	57.8
	REVERSE	GGCACACAATTTTGGAGCAG

Multiple primer sets were designed for loci where multiple read hits allowed potential amplification of different introns. Primer set names correspond to the orthologs of these genes in Arabidopsis. Listed annealing temperatures were used in amplifications of Asclepias samples. An annealing temperature of 55°C was used for all loci for amplifications of other Apocynaceae samples.

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ISSN: 1471-2164

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