Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean

Table 7 Sequence of primers/adaptors used for ITS, AFLP and SSRs

Sequence of primers used for ITS	Name of primer	Ann. temp. (°C)	Motive	Length of PCR product (bp)	Source
5′-CCTTATCATTTAGAGGAAGGAG-3′	ITS5a	52		700	[67]
5′-TCCTCCGCTTATTGATATGC-3′	ITS4				[68]
Sequence of adaptors and primers used for AFLP
5′-CTCGTAGACTGCGTACC-3′	EcoRI adaptors				[69]
5′-AATTGGTACGCAGTCTAC-3′
5′-GACGATGAGTCCTGAG-3′	MseI adaptors
5′-TACTCAGGACTCAT-3′
5′-GACTGCGTACCAATTCA-3′ (EcoRI + A)	Pre-selective primers
5′-GATGAGTCCTGAGTAAA-3′ (MseI + A)
EcoRI + ACA/MseI + ATC (set1)	Final amplification			50-500
EcoRI + ACC/MseI + ATC (set2)
EcoRI + ACA/MseI + ACA (set3)
EcoRI + ACC/MseI + ACA (set4)
Sequence of primers used for SSRs
5′-GAATGGGAAGGTGAAAGAG-3′	HO5	59	(AT)_n(GA)_n	260-296	[70]
5′-CACGGCACTGTTCATCTAC-3′
5′-ATAACCAAAGCCTCCCAAGC-3′	HO8	52	(GA)_n	156-186
5′-AAATATCAAACGCCCCTCAC-3′
5′-CAACTAACCAAACGAGAAAC-3′	HO36	59	(GA)_nGC(GA)_n	220-240
5′-AACCTTGACACCTGCTAATA-3′
5′-ATCGAACCCAATAGACACCAG-3′	HO48	59	(GA)_n	196-246
5′-CAGGCAACTTAGCAAGAAACT-3′
5′-AGATAAGTTTCACTCCTGTG-3′	HO51	46	(GA)_n	141-175
5′-ACCAGAACCAATCAAGAT-3′

There are four primer pairs used for final amplification in AFLP and five primer pairs used to amplify five loci in SSRs. Ann. temp. Annealing temperature; bp, base pairs.

ISSN: 2730-7182