Chin Bull Bot ›› 2015, Vol. 50 ›› Issue (1): 55-71.doi: 10.3724/SP.J.1259.2015.00055

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

Molecular Evolution of Chalcone Synthase Gene Superfamily in Plants

Ying Bao1, 2, *, Changfeng Guo1, Shaohua Chen1, Mei Liu1   

  1. 1School of Life of Sciences, Qufu Normal University, Qufu 273165, China
    2State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
  • Received:2013-11-04 Accepted:2014-02-23 Online:2015-04-09 Published:2015-01-01
  • Contact: Bao Ying E-mail:baoyingus@126.com
  • About author:

    ? These authors contributed equally to this paper

Abstract:

The chalcone synthase (CHS) gene superfamily, also known as plant-specific type III polyketide synthase gene superfamily, encodes many important enzymes that can catalyze and synthesize various plant secondary metabolites with diverse structures and different biological activities. These metabolites play key roles in plant growth, reproduction, and plant adaptation to the environment. To fully understand the basic evolutionary rules of the CHS gene superfamily in plants and reconstruct its evolutionary history, we performed bioinformatics analysis of CHS genes in 14 plant species with whole-genome data. We performed a BLAST search to identify the gene members of the CHS superfamily. The possible expansion mechanisms and functional divergences of the members were characterized, and the evolution- ary trend of the superfamily was explored. We identified 144 genes with expression information; all are expressed in 9 land plants but not 5 algae. Phylogenetic analysis revealed that the CHS gene superfamily had an ancient origin and complicated evolutionary history. It probably appeared in early terrestrial plants to adapt to the complex environment, then experienced lineage-specific expansions or gene loss during evolution, and finally was fixed in different plant taxa through functional divergences. In addition, evolutionary testing showed that despite diverse genetic differentiation within the CHS superfamily, the whole superfamily was still filtered by strong purifying selection and no single amino acid site within an individual gene was affected by positive selection.

Table 1

Genes in CHS superfamily identified from 13 plants genomes by BLAST searching"

Species Locus No. Gene ID Strand Chromosome Duplication pattern
Arabidopsis thaliana 1 AT1G02050 - 1
2 AT4G00040 + 4
3 AT4G34850 + 4
4 AT5G13930 + 5
Medicago truncatula 1 MT1G097900 + 1 Tandem
2 MT1G097910 + 1 Tandem
3 MT1G098140 + 1 Tandem
4 MT1G098150 + 1 Tandem
5 MT2G058470 - 2
6 MT3G083910 - 3 Tandem and block
7 MT3G083920 - 3 Tandem and block
8 MT3G086260 + 3
9 MT4G078730 + 4
10 MT5G007720 + 5 Tandem
11 MT5G007730 + 5 Tandem
12 MT5G007740 + 5 Tandem
13 MT5G007760 + 5 Tandem
14 MT5G007770 + 5 Tandem
15 MT7G016700 + 7 Tandem
16 MT7G016720 - 7 Tandem
17 MT7G016780 + 7 Tandem
18 MT7G016800 + 7 Tandem
19 MT7G016820 + 7 Tandem
20 MT7G084300 - 7
21 MT8G085200 + 8 Block
Populus trichocarpa 1 PT00G02200 - Scaffold_955
2 PT01G06410 + Scaffold_1 Block
3 PT01G14120 + Scaffold_1 Tandem and block
4 PT01G14130 + Scaffold_1 Tandem and block
5 PT02G14050 - Scaffold_2 Block
6 PT03G16580 + Scaffold_3 Tandem and block
7 PT03G16590 + Scaffold_3 Tandem and block
8 PT03G16600 + Scaffold_3 Tandem and block
9 PT04G16510 + Scaffold_4 Block
10 PT05G15150 - Scaffold_5 Tandem
11 PT09G12950 + Scaffold_9 Block
12 PT12G12680 + Scaffold_12 Block
13 PT14G05350 - Scaffold_14 Block
14 PT14G14010 - Scaffold_14
Vitis vinifera 1 VV03G05390 + 3
2 VV05G00090 + 5
3 VV10G06850 + 10 Tandem
4 VV10G06860 + 10 Tandem
5 VV14G13530 + 14
6 VV15G00770 - 15
7 VV16G00180 - 16 Tandem
8 VV16G00200 - 16 Tandem
表1 (续) Table 1 (continued)
Species Locus No. Gene ID Strand Chromosome Duplication pattern
9 VV16G00220 - 16 Tandem
10 VV16G00240 - 16 Tandem
11 VV16G00260 - 16 Tandem
12 VV16G00280 + 16 Tandem
13 VV16G00290 - 16 Tandem
14 VV16G00310 - 16 Tandem
15 VV16G00320 - 16 Tandem
16 VV16G00330 - 16 Tandem
17 VV16G00340 - 16 Tandem
18 VV16G00350 - 16 Tandem
19 VV16G00360 - 16 Tandem
20 VV16G00370 - 16 Tandem
21 VV16G00380 + 16 Tandem
22 VV16G00390 + 16 Tandem
Oryza sativa 1 OS01G41834 - 1
2 OS04G01354 - 4
3 OS04G23940 - 4
4 OS05G12180 - 5 Tandem
5 OS05G12190 - 5 Tandem
6 OS05G12210 - 5 Tandem
7 OS05G12240 - 5 Tandem
8 OS05G41645 + 5
9 OS07G11440 - 7
10 OS07G17010 + 7
11 OS07G22850 - 7
12 OS07G31750 - 7 Tandem
13 OS07G31770 - 7 Tandem
14 OS07G34140 - 7 Tandem
15 OS07G34190 - 7 Tandem
16 OS07G34260 - 7 Tandem
17 OS10G07040 + 10
18 OS10G07616 + 10
19 OS10G08620 + 10 Tandem
20 OS10G08670 + 10 Tandem
21 OS10G08710 + 10 Tandem
22 OS10G09860 - 10
23 OS10G34360 + 10
24 OS11G32540 - 11 Tandem
25 OS11G32580 - 11 Tandem
26 OS11G32610 + 11 Tandem
27 OS11G32620 - 11 Tandem
28 OS11G32650 - 11 Tandem
29 OS11G35930 + 11
30 OS12G07690 - 12
Zea mays 1 ZM01G41780 - 1 Block
2 ZM02G42820 - 2 Tandem and block
3 ZM02G42850 - 2 Tandem and block
4 ZM02G45550 + 2
表1 (续) Table 1 (continued)
Species Locus No. Gene ID Strand Chromosome Duplication pattern
5 ZM03G09860 + 3 Tandem
6 ZM03G09890 - 3 Tandem
7 ZM03G09930 - 3 Tandem
8 ZM04G30630 + 4 Tandem and block
9 ZM04G30650 + 4 Tandem and block
10 ZM04G32440 - 4
11 ZM05G09820 + 5 Block
12 ZM05G24850 + 5
13 ZM07G22450 - 7 Block
Physcomitrella patens 1 PP00001G00030 - Scaffold_1
2 PP00020G01360 - Scaffold_20
3 PP00022G00030 + Scaffold_22
4 PP00025G01920 + Scaffold_25 Tandem
5 PP00025G01930 - Scaffold_25 Tandem
6 PP00034G01040 + Scaffold_34
7 PP00038G00030 - Scaffold_38
8 PP00039G01610 - Scaffold_39
9 PP00061G00280 - Scaffold_61
10 PP00076G01020 + Scaffold_76
11 PP00228G00140 - Scaffold_228 Tandem
12 PP00292G00010 - Scaffold_292
13 PP00303G00060 - Scaffold_303 Tandem
14 PP00303G00070 + Scaffold_303 Tandem
15 PP00304G00340 - Scaffold_304
16 PP00365G00100 - Scaffold_365 Tandem
17 PP00365G00120 + Scaffold_365 Tandem
18 PP00425G00060 - Scaffold_425 Tandem
19 PP00426G00290 - Scaffold_426
20 PP00463G00060 - Scaffold_463 Tandem
21 PP00463G00070 + Scaffold_463 Tandem
22 PP00463G00100 - Scaffold_463 Tandem
23 PP00500G00030 - Scaffold_500
Selaginella moellendorffii 1 SM00001G06800 - Scaffold_1
2 SM00017G03910 - Scaffold_17
3 SM00007G01560 - Scaffold_7
4 SM00068G00810 - Scaffold_68
Ostreococcus lucimarinus - - - - -
O. tauri - - - - -
Micromonas sp. RCC299 - - - - -
Volvox carteri - - - - -
Chlamydomonas reinhardtii - - - - -

Table 2

Contigs contained genes of CHS superfamily in Pinus taeda genome"

No. Contig Length
(bp)
Score bits Strand Identities E-value Sequence
information
1 Ctg7180044571087 2 448 1 564 - 1 134/1 301 (87%) 0 Complete
2 Ctg7180044837494 4 493 1 535 - 1 119/1 301 (86%) 0 Complete
3 Ctg7180046059388 2 761 1 736 - 1 185/1 328 (89%) 0 Complete
4 Ctg7180055825794 3 986 1 000;
241
-
-
821/999 (82%); 180/211 (85%) 0
7e-60
Complete
5 Ctg7180056125030 4 720 1 476;
378
-
-
976/1 077 (91%); 226/237 (95%) 0
4e-101
Complete
6 Ctg7180057362889 39 003 1 893 - 1 265/1 402 (90%) 0 Complete
7 Jtg7180055651041f_7180057409216f 5 769 1 337;
309
-
-
891/991 (90%); 215/244 (88%) 0
2e-80
Complete
8 Jtg7180057127125f_7180046406791r 10 190 1 577 - 1 123/1 284 (87%) 0 Complete
9 Ctg7180057114010 6 665 1 342 + 1 077/1 298 (83%) 0 Complete
10 Ctg7180057423160 15 081 1 471 + 1 087/1 271 (86%) 0 Complete
11 Jtg7180046403543f_7180056907730f 6 806 2 006 + 1 288/1 401 (92%) 0 Complete
12 Jtg7180043014796r_7180045416866r 5 549 717;
149
+
+
762/1 001 (76%); 141/180 (78%) 0
3e-32
Complete
13 Ctg7180057238333 10 113 1 712;
342
-
-
966/977 (99%); 194/197 (98%) 0
2e-90
Complete
14 Ctg7180055304970 1 885 1 265 - 911/1 039 (88%) 0 Fragment
15 Ctg7180044078159 1 566 1 209 - 875/1 000 (88%) 0 Fragment
16 Ctg7180054149681 1 521 951 + 646/724 (89%) 0 Fragment
17 Ctg7180040742080 576 872 - 539/576 (94%) 0 Fragment
18 Ctg7180055755024 954 805 + 537/596 (90%) 0 Fragment
19 Ctg7180054149682 656 792 + 507/552 (92%) 0 Fragment
20 Ctg7180057090732 1 429 735 - 766/1 001 (77%) 0 Fragment
21 Ctg7180056804266 2 400 735 + 766/1 001 (77%) 0 Fragment
22 Ctg7180055304969 1 187 726 - 476/524 (91%) 0 Fragment
23 Deg7180050331267 530 704 + 474/530 (89%) 0 Fragment
24 Ctg7180047225082 2 089 704 + 756/998 (76%) 0 Fragment
25 Ctg7180057563133 1 376 675 + 753/1 002 (75%) 0 Fragment
26 Deg7180049910668 707 659 - 574/706 (81%) 0 Fragment
27 Ctg7180040473811 2 084 650 + 734/981 (75%) 0 Fragment
28 Deg7180050301638 1 145 623 + 510/616 (83%) 6e-175 Fragment
29 Ctg7180046407516 2 023 600 + 736/1 002 (73%) 6e-168 Fragment
30 Ctg7180056729621 1 548 583 + 654/871 (75%) 5e-163 Fragment
31 Ctg7180055812743 7 348 583 - 730/999 (73%) 5e-163 Fragment
32 Ctg7180056199763 7 255 574 + 722/987 (73%) 3e-160 Fragment
33 Ctg7180055845812 12 473 563 - 667/900 (74%) 5e-157 Fragment
34 Ctg7180053679462 1 148 554 - 659/891 (74%) 2e-154 Fragment
35 Ctg7180050291419 893 554 + 609/806 (76%) 2e-154 Fragment
36 Ctg7180040305101 946 553 + 623/833 (75%) 8e-154 Fragment
37 Ctg7180056889828 1 745 545 + 622/831 (75%) 1e-151 Fragment
38 Ctg7180040359262 801 544 + 536/691 (78%) 4e-151 Fragment
39 Ctg7180038459346 430 533 - 376/430 (87%) 8e-148 Fragment
40 Ctg7180038501054 559 522 - 453/555 (82%) 1e-144 Fragment
41 Ctg7180050814991 1 172 509 + 600/808 (74%) 9e-141 Fragment
42 Ctg7180057409908 1 097 508 + 343/384 (89%) 3e-140 Fragment
表2 (续) Table 2 (continued)
No. Contig Length
(bp)
Score
bits
Strand Identities E-value Sequence
information
43 Ctg7180056950914 6 228 1 357 + 1 092/1 318 (83%) 0 Nonsense mutation
44 Ctg7180056550739 18 693 1 342 - 1 076/1 293 (83%) 0 Nonsense mutation
45 Jtg7180056551170f_7180056551171f 9 504 1 198 - 1 060/1 326 (80%) 0 Nonsense mutation
46 Ctg7180039529527 1 759 677 + 754/1 001 (75%) 0 Nonsense mutation
47 Jtg7180057668388f_7180057668389f 5 289 661 + 734/975 (75%) 0 Nonsense mutation
48 Ctg7180044573223 1 796 650 - 747/1 001 (75%) 0 Nonsense mutation
49 Ctg7180056441624 5 881 600 + 739/1 002 (74%) 6e-168 Nonsense mutation
50 Jtg7180056265080f_7180046063071r 7 390 513 + 714/992 (72%) 7e-142 Nonsense mutation
51 Jtg7180057409910f_7180057409911f 20 052 1 393 + 1 080/1 281 (84%) 0 Frame shift

Figure 1

Three duplication patterns of genes occurred in CHS superfamily (A) Patterns of tandem duplication in Vitis vinifera, Medicago truncatula, Oryza sativa and Physcomitrella patens; (B) Patterns of block duplication between Populus trichocarpa and V. vinifera; (C) Pattern of block and tandem duplication in P. trichocarpa; (D) Pattern of possible transposition duplication in Arabidopsis thaliana. Arrows represent genes with direction in genomes; Homologues shows in same colors; Target genes in CHS superfamily are framed"

Figure 2

Phylogram resulting of the CHS superfamily from maximum likelihood analysis with an amino acid substitution model LG+G+F (A) Whole tree; (B)-(E) Clades in detail. Numbers beside the branches refer to the bootstrap values (>50%) based on 100 replications. Gene information is shown in Table 1 and 2."

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