Table 1.
Sixteen sets of orthologous and homoeologous sequences isolated from diploid and allopolyploid Gossypium
| Locus | Linkage group* | Known gene or database match† | E value‡ | L§ | LA¶ | LS∥ | Forward primer sequence/ reverse primer sequence |
|---|---|---|---|---|---|---|---|
| A1286 | HA 10 | Unknown | — | 294 | — | — | GTACTGCGGTAGACATGCATGAAAC/ACTCTTCTTTAGCATCAGCTTCACCA |
| A1341 | HA 7A | Unknown | — | 624 | — | — | GCATGCTGAATTGACAGAACCAGCY/CACTCACAAAGTTATGCCGGATGY |
| A1520 | HA 6 | Unknown | — | 957 | — | — | GGCTGCAAAACCCCTAGGATTAGTY/CAAGCCAGGCAAGCACTCCAAGA |
| A1550 | HA 9 | Arabidopsis thaliana aldehyde dehydrogenase (2961384) | 8.0E-16 | 1,448 | 139 | 1,070 | CCACCTCAGGCAAGGTTATCAY/GGGATCAATGTGGCCATGTR |
| A1623 | HA 5 | Unknown | — | 840 | — | — | GATATTGAATGATCAACATGTGCGAT/CTTTTACCTGCTGTGATGCCCAGT |
| A1625 | HA 1 | Unknown | — | 1,061 | — | — | CGATTCCCTACCAAATCGAGGT/CATGGGACCCTGAAAGTTGAA |
| A1713 | HA 6 | Unknown | — | 702 | — | — | GAGGAGGAAGTTTGATCAACCACTG/GGGTGCTTATGGTTATACAGGTGC |
| A1751 | HA 10 | Lycopersicon esculentum subtilisin protease (1771162) | 1.0E-70 | 807 | 587 | 220 | GCTGGAATGCTGGTTGTTATGAC/GATGAGCTGCCTTCAACAAAGC |
| A1834 | HA 8b | A. thaliana α-mannosidase precursor (1888357) | 1.2E-23 | 882 | 162 | 654 | TCACTAAAGAACCCATGTGGAT/AGGGATCAATTTGCCAACCAA |
| G1121 | HA 3 | Homo sapiens putative brain protein, (3043668) | 2.0E-06 | 749 | 670 | 216 | CTGGATCAGCCATATGATGACAGGY/TCAACCTAGTGGGGAGTGCTY |
| G1134 | HA 8b | Unknown | — | 546 | — | — | CAGCTGGAGGATGGTTAGCTTCTCY/GACTTGCACGTAAAGCACGAACC |
| G1262 | HA 9 | Hordeum vulgare P-glycoprotein (2292907) | 1.0E-103 | 888 | 670 | 216 | GGCGGCAGGCTAAGCACTTCY/CGGAGGTCATACTTCCAGCTTY |
| AdhA | HA 8C | AdhA (similar to 1840425 from Vitis vinifera) | 1.0E-85 | 951 | 464 | 468 | CTTCACTGCTTTATGTCACACT/GGACGCTCCCTGTACTCC |
| AdhC | HA 7B | AdhC (similar to 2570182 from Arabis gemmifera) | 4.0E-62 | 1,680 | 873 | 765 | CTGCKGTKGCATGGGARGCAGGGAAGCC/ GCACAGCCACACCCCAACCCTG |
| CelA1 | HA 10 | CelA1 (similar to 1706956 from G. hirsutum) | 8.0E-31 | 1,096 | 440 | 604 | GATGGAATCTGGGGTTCCTGTTTGC/GGGAACTGATCCAACACCCAGGA |
| CelA2 | HA 1 | CelA2 (similar to 1706956 from G. hirsutum) | 1.0E-22 | 1,180 | 460 | 682 | GATGGAATCTGGGGTTCCTGTTTGC/GGGAACTGATCCAACACCCAGGA |
*Homoeologous assemblages (HA) from Brubaker et al. (30).
†Identities are based upon tblastx searches of GenBank NR database; protein sequence identification number (PID) in parentheses.
‡Smallest sum probability scores from tblastx search.
§Aligned sequence length in base pairs.
¶Number of synonymous sites, excluding gapped sites.
∥Number of nonsynonymous sites, excluding gapped sites.