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Table 2 Sequence origins, homology and primer sequences of 24 Conserved Avian Microsatellite ( CAM ) loci

From: High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species

Marker

Sequence origins: ZF: zebra finch contig name & position CH: chicken chromosome & base pair location*

ZF seq. length (bp) and similarity to CH (E-value)

Homology to ESTs or genes Ŧ

Primer sequence (5′- 3′) and fluoro-label ¥

No. of degen. bases in primer pair

Primer seq. similarity to CH (%ID) (& number of bases mis-matching) Ψ

CAM-01

ZF: Contig4.1379:6555-6992

437

Gene

[F] [HEX]AAAGGCCAAGRCCAGTATG

1

[F] 100

 

CH: chr2:67828480-67828907

9E-147

 

[R] CTCTCATCCACCCTGTTAGC

 

[R] 100

CAM-02

ZF: Contig5.1371:163550-163981

431

None

[F] [6FAM]GAATTAAAGAYAGCAGATGCAGG

1

[F] 100

 

CH: chr7:22132454-22132893

1.1E-96

 

[R] AGCTGATGAAATGAGAATGCAG

 

[R] 100

CAM-03

ZF: Contig5.1597:35280-35767

487

None

[F] [HEX]ATTAGCATAGCTCAGCATTGCC

1

[F] 91 (2)

 

CH: chr7:24391832-24392259

2.2E-70

 

[R] CGAGCATTCAAMCCTGTCATC

 

[R] 95 (1)

CAM-04

ZF: Contig8.649:3118-3539

421

None

[F] [6FAM]TACCTCTGGCYAAGGAACTG

1

[F] 90 (2)

 

CH: chr1:133721521-133721942

6E-133

 

[R] GCTCAGAACATCAATCACTGC

 

[R] 100

CAM-05

ZF: Contig12.77:11232-11665

433

EST & gene

[F] [6FAM]TTACACAGACTGCAAACCGC

1

[F] 100

 

CH: chr1:47660443-47660868

2.4E-72

 

[R] CTGTTKCTCTAGTAATGAGATCCTG

 

[R] 92 (2)

CAM-06

ZF: Contig12.342:17413-17858

445

Gene

[F] [HEX]GTGATGGTCCAGGTCTTGC

0

[F] 100

 

CH: chr1:52304006-52304445

9E-115

 

[R] CAAGAGGAACAGATGAGGGTC

 

[R] 100

CAM-07

ZF: Contig12.442:2629-3062

433

EST & gene

[F] [HEX]AAATGATGAGRTCTGGGTGAG

2

[F] 100

 

CH: chr1:53412026-53412463

2E-113

 

[R] CCATTTCCAAGWGATTTGC

 

[R] 100

CAM-08

ZF: Contig13.893:13419-13850

431

EST & gene

[F] [6FAM]AGAARAAGCCACCCTCACAG

1

[F] 100

 

CH: chr10:516461-516890

5E-79

 

[R] CTCGTTTCCATTGGCGTTG

 

[R] 95 (1)

CAM-09

ZF: Contig15.537:32597-33018

421

None

[F] [HEX]AGAYACACAGCCACCCCAGAG

3

[F] 86 (3)

 

CH: chr4:17039238-17039667

1.6E-79

 

[R] CACWTGTATCCACAYGCTGAC

 

[R] 90 (2)

CAM-10

ZF: Contig16.130:3866-4309

429

EST & gene

[F] [6FAM]TATCCMGAGAATGGGCATC

2

[F] 89 (2)

 

CH: chr13:1070809-1071238

4.4E-67

 

[R] KGCTCTCATTGTCATGCTG

 

[R] 95 (1)

CAM-11

ZF: Contig17.242:5423-5868

445

EST & gene

[F] [HEX]TGGTACAGGGACAGCAAACC

1

[F] 100

(Z-linked)

CH: chrZ:7888318-7888739

1.7E-89

 

[R] AGATGCTGRGAGCGGATG

 

[R] 100

CAM-12

ZF: Contig23.425:77718-78157

439

None

[F] [6FAM]TGGCARTAAWTCCAGAGATTACC

3

[F] 100

 

CH: chr2:62785492-62785919

1E-95

 

[R] CTGRCATTTGTCTTAAGCGTG

 

[R] 95 (1)

CAM-13

ZF: Contig28.55:8348-8785

437

EST & gene

[F] [HEX]TCAAATACAGCAGCAGGCAG

0

[F] 100

 

CH: chr6:28449965-28450408

4E-140

 

[R] TTCATTACCAAACAGCATCCAG

 

[R] 100

CAM-14

ZF: Contig32.413:24503-24950

447

Gene

[F] [6FAM]GYAAGTGAAAGCTAAAGAAAGCC

1

[F] 100

 

CH: chr9:5323789-5324214

2.3E-92

 

[R] GGCAGTTCCAGCCATTTAC

 

[R] 100

CAM-15

ZF: Contig49.62:16781-17206

425

Gene

[F] [6FAM]SGACGACTCCTTTATTTCCC

2

[F] 90 (2)

 

CH: chr1:73032096-73032543

9E-105

 

[R] TTCTGACTTCCYCAGGTAACAC

 

[R] 100

CAM-16

ZF: Contig50.513:25871-26302

431

Gene

[F] [HEX]AGCCTTGATMTTGGGAAGAGC

2

[F] 90 (2)

 

CH: chr17:4598995-4599424

1.1E-85

 

[R] ATCCATACTCYGTGCAACCTG

 

[R] 100

CAM-17

ZF: Contig56.179:11880-12303

423

EST

[F] [6FAM]CGGGTTGTAATCAAGAAGATGC

0

[F] 100

 

CH: chr3:10551236-10551663

5E-141

 

[R] CTGCGGAGCAATTAACGC

 

[R] 100

CAM-18

ZF: Contig61.97:37926-38358

432

EST & gene

[F] [HEX]TTAAGAAGTTTACACCCAGCG

0

[F] 100

 

CH: chr3:31888225-31888655

1E-106

 

[R] GCTAAATAACAGAGCCAGGAAG

 

[R] 100

CAM-19

ZF: Contig69.248:5308-5739

431

EST & gene

[F] [6FAM]TCTTGGAGGCAGATARGAAGTG

1

[F] 100

 

CH: chr1:199733800-199734239

4E-119

 

[R] GAGCAAGCAAAGATCACAAGC

 

[R] 100

CAM-20

ZF: Contig70.196:1579-2012

433

EST & gene

[F] [HEX]TAACAGGCAGGAATGCAGG

0

[F] 100

 

CH: chr24:2939427-2939862

9E-105

 

[R] TCAGCCAGTGTTGGAGGTC

 

[R] 100

CAM-21

ZF: Contig74.100:2226-2651

425

Gene

[F] [6FAM]TGGGAGAACATTATAGCGTGAG

1

[F] 100

 

CH: chr2:2408229-2408652

1.1E-96

 

[R] TTGAAATGRGAACCACGGAC

 

[R] 95 (1)

CAM-22

ZF: Contig75.34:11916-12343

427

None

[F] [HEX]RAGRGCCACTTTCACTCCTG

3

[F] 90 (2)

 

CH: chr18:6214289-6214714

1.2E-76

 

[R] ATGCTGTGACACTKGGAGGC

 

[R] 100

CAM-23

ZF: Contig83.70:49198-49633

435

EST & gene

[F] [6FAM]CTCCACTTAGCTTGTAAATGCAC

1

[F] 96 (1)

 

CH: chr6:31243934-31244369

2E-142

 

[R] CCAAGRAGTGCCCTAGATGTC

 

[R] 100

CAM-24

ZF: Contig122.74:8163-8588

425

None

[F] [HEX]CCCACTTCAGTCTTCAGAGC

0

[F] 100

 

CH: chr1:2092872-2093301

1.8E-59

 

[R] TGGAGTATTTGGGATTGGAG

 

[R] 100

  1. *, the zebra finch sequences were isolated by a search of the unassembled contigs and super contigs of the zebra finch genome and the chicken sequences were isolated by a search of the assembled chicken genome (v2.1). The sequence of each locus is provided in Additional file 2.
  2. bp, base pairs;
  3. ZF, zebra finch Taeniopygia guttata;
  4. CH, chicken Gallus gallus;
  5. F, forward primer sequence;
  6. R, reverse primer sequence
  7. ¥, The forward and reverse primer sequences match 100% to zebra finch and 86–100% to chicken Gallus gallus when the degenerate bases are accounted for. The degenerate bases used in the primer sequences shown in bold and underlined, R = A or G, Y = C or T, M = A or C, S = C or G, W = A or T, K = G or T;
  8. Ψ, calculated by dividing the number of bases matching chicken (after accounting for the degenerate bases) by the total length of the primer sequence;
  9. Ŧ, assessed for (a) similarity to sequences in the NCBI nucleotide EST and nr/nt databases identified using blastn (distant homologies) settings and (b) for similarity to protein coding regions in the CH & ZF assembled genomes which was identified by the presence of exons within 5 kb of the source sequence (searches performed 30/09/2011). Details of the sequence homologues found are provided in Additional file 6.
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BMC Genomics

ISSN: 1471-2164

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