Table 2

Divergence between Paralogous CCCH Genes Pairs in Populus
No. Gene 1 Gene 2 Ks Ka Ka/Ks Duplication Motif/Gene structure Characteristics Gene Expression
1 PtC3H1 PtC3H2 0.3237 0.0906 0.2797 O 1 AA
2 PtC3H3 PtC3H4 0.2939 0.0477 0.1624 W 1 AA
3 PtC3H5 PtC3H6 0.0416 0.0088 0.2104 T 1 AA
4 PtC3H8 PtC3H10 0.2961 0.1455 0.4913 W 2 AB
5 PtC3H9 PtC3H65 0.3851 0.1906 0.4950 W 2 No
6 PtC3H11 PtC3H12 0.2979 0.1402 0.4706 W 2 AB
7 PtC3H13 PtC3H14 0.4247 0.1629 0.3835 W 2 No
8 PtC3H15 PtC3H16 0.3063 0.0483 0.1577 W 2 AC
9 PtC3H17 PtC3H18 0.3111 0.0603 0.1939 W 1 AC
10 PtC3H22 PtC3H23 0.2919 0.1136 0.3893 W 1 AB
11 PtC3H25 PtC3H72 0.3609 0.0571 0.1582 O 1 No
12 PtC3H26 PtC3H29 0.0125 0.0078 0.6247 O 2 No
13 PtC3H32 PtC3H34 0.1084 0.0482 0.4446 O 1 No
14 PtC3H35 PtC3H38 0.2903 0.0678 0.2334 W 1 AC
15 PtC3H36 PtC3H39 0.3407 0.0632 0.1855 W 1 No
16 PtC3H42 PtC3H43 0.3935 0.1055 0.2681 W 3 No
17 PtC3H44 PtC3H83 0.2825 0.0712 0.2521 O 1 AC
18 PtC3H46 PtC3H47 1.4585 0.7131 0.4889 O 2 AC
19 PtC3H48 PtC3H77 0.0234 0.0048 0.2064 T 1 No
20 PtC3H49 PtC3H50 0.2805 0.0684 0.2440 O 3 AB
21 PtC3H51 PtC3H52 0.2720 0.0812 0.2985 W 1 No
22 PtC3H54 PtC3H55 0.2172 0.0637 0.2930 W 2 No
23 PtC3H57 PtC3H58 0.1967 0.1130 0.5745 W 3 AA
24 PtC3H60 PtC3H61 0.2951 0.1372 0.4650 W 2 AB
25 PtC3H62 PtC3H64 0.2644 0.1031 0.3900 W 3 No
26 PtC3H66 PtC3H68 0.2405 0.0373 0.1552 W 1 AC
27 PtC3H67 PtC3H69 0.3284 0.1028 0.3131 O 1 No
28 PtC3H70 PtC3H71 0.2795 0.0818 0.2925 W 1 AB
29 PtC3H74 PtC3H75 0.2405 0.0364 0.1512 W 1 AB
30 PtC3H79 PtC3H80 0.2565 0.1364 0.5318 O 1 No
31 PtC3H81 PtC3H82 0.2465 0.1066 0.4326 W 1 AC
32 PtC3H84 PtC3H86 0.4725 0.0678 0.1435 W 1 AD
33 PtC3H85 PtC3H87 2.4099 0.1624 0.0674 O 2 AD
34 PtC3H90 PtC3H91 0.2513 0.0496 0.1972 W 1 AB

Gene pairs were identified at the terminal nodes (>80‚ÄČ% identical) of the phylogenetic tree shown in Figure 1. Synonymous (Ks) and nonsynonymous substitution (Ka) rates are presented for each pair. Gene pairs created by tandem duplication (T), whole genome duplication (W), or other (O) events are indicated in the table. Motif/Gene structure characteristics of gene pairs were divided into three groups: 1, identical exon/intron structure and motif composition; 2, identical motif and variable gene structure; 3, less conserved exon/intron structure and motif composition. Gene expression patterns based on microarray data (GSE13990) are categorized into four classes: AA, both of duplicates were expressed in non-overlapping tissues; AB, both duplicates had the same expression patterns; AC, expression tissues of one duplicate completely covered the other; AD, expression tissues of both duplicates were overlapping but different; No, no data for one duplicate is present in the microarray.

Chai et al.

Chai et al. BMC Genomics 2012 13:253   doi:10.1186/1471-2164-13-253

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