Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)

BMC Genomics

Table 2 Divergence between Paralogous CCCH Genes Pairs in Populus

No.	Gene 1	Gene 2	K_s	K_a	K_a/K_s	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 % 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.

ISSN: 1471-2164