Table 2.
Sequence origins, homology and primer sequences of 24 Conserved Avian Microsatellite ( CAM ) loci
| 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 |
*, 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.
bp, base pairs;
ZF, zebra finch Taeniopygia guttata;
CH, chicken Gallus gallus;
F, forward primer sequence;
R, reverse primer sequence
¥, 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;
Ψ, calculated by dividing the number of bases matching chicken (after accounting for the degenerate bases) by the total length of the primer sequence;
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.