Stephanie A. J. Preston, Deborah A. Dawson, Gavin J. Horsburgh, Ben J. Hatchwell
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Characterisation of microsatellite loci in the rifleman (Acanthisitta chloris, Acanthisittidae, AVES) and their predicted genome locations
STEPHANIE A. J. PRESTON, DEBORAH A. DAWSON, GAVIN J. HORSBURGH, BEN J. HATCHWELL
Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
* * S.A.J. Preston E-mail:
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Online Resource 1
Table 1. Additional microsatellite loci characterised in 4 unrelated rifleman Acanthisitta chloris individuals (2 male and 2 female) but abandoned from further testing
(a) Additional newly isolated rifleman microsatellite loci
Locus / EMBL Accession Number / Repeat Motif / Primer Sequence (5’-3’) / Tm / Ta / Fluoro Label (F) / Expected/ Observed Size (bp) / N / A / Chromosome Location / BLAST E Value / Marker Status /Ach092 / HE599034
Ach18F07 / (GT)12 / F:TCCTTGGAAAGGGATTAGGG
R:CCACTTCAGCTCAAATCAACAC / 60.3
59.8 / 60 / HEX / 135/
- / (4) / -- / No matches (Gga)
TguZ, 66784737† / -
1.0e-21 WGS† (0.0) / Failed to amplify in males and females
Ach115 / HE599097
Ach21C06 / (ATCT)14 / F:ATGTGTCTCGAACACCTCCAG
R:TGCAAAGTCTCTGTTGGTTCC / 60.2
60.3 / 60 / 6FAM / 207/
202-214
378-390 / 4 / 6 / Gga8, 2291741†
Tgu8, 4792269 / 2.0e-50 WGS† (0.0)
2.6e-93 / Polymorphic but amplified two different loci
Ach122 / HE599064
Ach21D04 / (AC)17 / F:AGGGATTTAACAGAAAGGCAAAG
R:TCAACCAACTCCTTGACATCC / 60.0
60.0 / 60 / 6FAM / 222/
- / (4) / -- / Gga1, 183850561
Tgu1, 45621322 / 1.2e-109
8.9e-173 / Failed to amplify
Ach125 / HE599067
Ach21D10 / (GT)23 / F:ACCATGCAGTGAAGGAAAGG
R:CTTCTTGTGGCTACAGCCTTG / 60.1
60.1 / 60 / HEX / 217/
- / (4) / -- / No matches (Gga)
Tgu2, 12389296† / 7.0e-38 WGS† (0.0)
1.0e-28 WGS† (0.0) / Failed to amplify
Ach137 / HE599079
Ach21F05 / (CTTT)49 / F:TACGGGTGGTGATATCTTTCC
R:AGTGGAAAGGAGGTATGTAGCC / 58.8
58.7 / 60 / 6FAM / 330/
- / (4) / -- / No matches (Gga)
Tgu1, 43942064 / -
6.1e-112 / Failed to amplify
Ach193 / HE599135
Ach22G12 / (GT)28 / F:GATCTGAACTCAGGTCTACACTAATAAGC
R:CCTCCCACTTGTCCCTTAGTC / 60.5
60.0 / 60 / HEX / 360/
- / (4) / - / No matches (Gga)
Tgu2, 38049847 / 5.0e-21 WGS† (0.0)
4.2e-56 / Failed to amplify
Ach201 / HE599143
Ach23A05 / (AG)23 / F:ACAGAACTGCAACCTGTCAAG
R:ATAGGCTGGGAATTGAGTCAC / 58.0
58.1 / 60 / 6FAM / 193/
- / (4) / -- / Gga3, 58421687†
Tgu3, 58738733† / 4.0e-25 WGS† (0.0)
9.0e-64 WGS† (0.0) / Failed to amplify
(b) Additional published microsatellite loci
TG01-000 / Dawson et al., 2010 / 56 / 6FAM / 253/
201 / 4 / 1 / Gga1, 725367
Tgu1A, 206523 / 0.0
1.7e-197 / Monomorphic
TG01-040 / Dawson et al., 2010 / 56 / 6FAM / 286/
275 / 4 / 1 / Gga1, 45170091
Tgu1A, 42620504 / 1.3e-145
0.0 / Monomorphic
TG01-077 / Dawson et al., 2010 / 56 / HEX / 153/
152 / 4 / 1 / Gga1, 86284969
Tgu1, 95581733 / 0.0
0.0 / Monomorphic
TG01-092 / Dawson et al., 2010 / 56 / 6FAM / 183/
177 / 4 / 1 / Gga1, 101715086
Tgu1, 101715086 / 2.4e-294
0.0 / Monomorphic
TG01-114 / Dawson et al., 2010 / 56 / HEX / 182/
181 / 4 / 1 / Gga1, 123969711
Tgu1, 15302987 / 0.0
0.0 / Monomorphic
TG01-124 / Dawson et al., 2010 / 56 / 6FAM / 403/
400 / 4 / 1 / Gga1, 135576703
Tgu1, 32303776 / 4.8e-140
0.0 / Monomorphic
TG01-148 / Dawson et al., 2010 / 56 / HEX / 195/
188 / 4 / 1 / Gga1, 163900541
Tgu1, 65236877 / 9.1e-159
0.0 / Monomorphic
TG02-078 / Dawson et al., 2010 / 56 / HEX / 308/
287 / 4 / 1 / Gga2, 80089604
Tgu2, 82845909 / 0.0
0.0 / Monomorphic
TG02-088 / Dawson et al., 2010 / 56 / 6FAM / 266/
255 / 4 / 1 / Gga2, 90692690
Tgu2, 93538047 / 0.0
0.0 / Monomorphic
TG02-120 / Dawson et al., 2010 / 56 / 6FAM / 230/
231 / 4 / 1 / Gga2, 125741769
Tgu2, 127242053 / 3.2e-251
0.0 / Monomorphic
TG03-002 / Dawson et al., 2010 / 56 / 6FAM / 127/
117 / 4 / 1 / Gga3, 2475598
Tgu3, 28478877 / 5.2e-128
0.0 / Monomorphic
TG03-031 / Dawson et al., 2010 / 56 / 6FAM / 208/
197 / 4 / 1 / Gga3, 36376128
Tgu3, 36376128 / 4.2e-255
0.0 / Monomorphic
TG03-035 / Dawson et al., 2010 / 56 / HEX / 213/
208 / 4 / 1 / Gga4, 35573626
Tgu4, 7353303 / 5.6e-131
0.0 / Monomorphic
TG03-098 / Dawson et al., 2010 / 56 / HEX / 235/
247 / 4 / 1 / Gga3, 103032357
Tgu3, 102966495 / 8.7e-293
0.0 / Monomorphic
TG04-012 / Dawson et al., 2010 / 56 / HEX / 150/
139 / 4 / 1 / Gga4, 11964133
Tgu4A, 17044351 / 6.6e-309
0.0 / Monomorphic
TG04-012A / Dawson et al., 2010 / 56 / 6FAM / 236/
233 / 4 / 1 / Gga4, 11862446
Tgu4A, 16934636 / 2.3e-252
0.0 / Monomorphic
TG04-041 / Dawson et al., 2010 / 56 / HEX / 173/
176 / 4 / 1 / Gga4, 41461742
Tgu4, 37987125 / 0.0
0.0 / Monomorphic
TG04-061 / Dawson et al., 2010 / 56 / HEX / 186/
190 / 4 / 1 / Gga4, 61990163
Tgu4, 20910674 / 8.9e-259
0.0 / Monomorphic
TG05-030 / Dawson et al., 2010 / 56 / HEX / 186/
179 / 4 / 1 / Gga5, 35196360
Tgu5, 32518629 / 2.3e-262
0.0 / Monomorphic
TG05-053 / Dawson et al., 2010 / 56 / HEX / 196/
191 / 4 / 1 / Gga5, 59348340
Tgu5, 61275929 / 5.9e-174
0.0 / Monomorphic
TG06-009 / Dawson et al., 2010 / 56 / 6FAM / 127/
119 / 4 / 1 / Gga6, 10668281
Tgu6, 3612453 / 1.8e-97
0.0 / Monomorphic
TG07-022 / Dawson et al., 2010 / 56 / HEX / 416/
443 / 4 / 1 / Gga7, 22591719
Tgu7, 11939763 / 2.1e-221
0.0 / Monomorphic
TG08-024
primer set 1 / Dawson et al., 2010 / 56 / HEX / 128/
126 / 4 / 1 / Gga8, 24356390
Tgu8, 21095625 / 0.0
0.0 / Monomorphic
TG08-024
primer set 2 / Dawson et al., 2010 / 56 / HEX / 243/
243 / 4 / 1 / Gga8, 24356390
Tgu8, 21095625 / 0.0
0.0 / Monomorphic
TG09-014 / Dawson et al., 2010 / 56 / 6FAM / 152/
148 / 4 / 1 / Gga9, 15901402
Tgu9, 16778581 / 0.0
0.0 / Monomorphic
TG12-015 / Dawson et al., 2010 / 56 / HEX / 283/
- / (4) / - / Gga12, 15500052
Tgu12, 16293509 / 6.6e-120
0.0 / Failed to amplify
TG13-016 / Dawson et al., 2010 / 56 / 6FAM / 136/
125 / 4 / 1 / Gga13, 17663220
Tgu13, 1151543 / 7.2e-140
0.0 / Monomorphic
TG22-001 / Dawson et al., 2010 / 56 / HEX / 269/
- / (4) / - / Gga22, 529626
Tgu22, 1428098 / 3.8e-168
0.0 / Failed to amplify
Tm, melting temperature
Ta, annealing temperature
N, number of unrelated rifleman Acanthisitta chloris individuals genotyped
A, number of alleles observed
Tgu zebra finch Taeniopygia guttata chromosome; Gga chicken Gallus gallus chromosome
Chromosome Location; † signifies where the location in zebra finch was assigned by an “indirect BLAST” i. e. we initially identified a homologous zebra finch whole genome shotgun (WGS) sequence which was then compared to the assembled genome of same species (method as described in Dawson et al. 2007). Duplicate hits to the “unknown” chromosome were ignored and regarded as artefacts of the assembly process.