Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (4): 167-178.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0970
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GUO Chun1,2(), SONG Gui-mei1,2, YAN Yan2, DI Peng1,2(), WANG Ying-ping1,2
Received:
2023-10-18
Online:
2024-04-26
Published:
2024-04-30
Contact:
DI Peng
E-mail:2069662120@qq.com;di@jlau.edu.cn
GUO Chun, SONG Gui-mei, YAN Yan, DI Peng, WANG Ying-ping. Genome Wide Identification and Expression Analysis of the bZIP Gene Family in Panax quinquefolius[J]. Biotechnology Bulletin, 2024, 40(4): 167-178.
基因 Gene | 上游引物Forward primer(5'-3') | 下游引物Reverse primer(5'-3') |
---|---|---|
PqbZIP1778 | TGATACATCTTCTGTGTCACCAATTCC | TGCCTCCTCTCAACAACCTTCTC |
PqbZIP3076 | GCCAGAGCCAGCAACAAGTTC | GATCTCTTCATCACTCTCCATACCTTC |
PqbZIP53695 | GTGCCACAACTCAACCAGAAGG | TCCGACTCCATCCAAGGTGTTC |
PqbZIP53753 | TGATGAACGATAACGGCATTGATAGG | TCCAGTAGAATATCCGCCAAGAGG |
GAPDH1-F | GCTATCAAGGAGGAGTCGGAGGG | CTGGACAGATGCCATGTGAACAA |
Table 1 Real-time fluorescence quantitative primers of PqbZIP gene family
基因 Gene | 上游引物Forward primer(5'-3') | 下游引物Reverse primer(5'-3') |
---|---|---|
PqbZIP1778 | TGATACATCTTCTGTGTCACCAATTCC | TGCCTCCTCTCAACAACCTTCTC |
PqbZIP3076 | GCCAGAGCCAGCAACAAGTTC | GATCTCTTCATCACTCTCCATACCTTC |
PqbZIP53695 | GTGCCACAACTCAACCAGAAGG | TCCGACTCCATCCAAGGTGTTC |
PqbZIP53753 | TGATGAACGATAACGGCATTGATAGG | TCCAGTAGAATATCCGCCAAGAGG |
GAPDH1-F | GCTATCAAGGAGGAGTCGGAGGG | CTGGACAGATGCCATGTGAACAA |
Fig. 3 Visualization of conservative domains in the PqbZIP family The total height of the letter stack at each position indicates the conservation of the sequence at that position. The height of a single letter in the letter stack indicates the relative frequency of the corresponding amino acid at that position
Fig. 4 Chromosomal localization and collinearity analysis of the bZIP gene family in P. quinquefolius The green line indicates duplicate pairs of bZIP genes in P. quinquefolius
Sequence | Method | Ka | Ks | Ka/Ks | Length/bp | Sequence | Method | Ka | Ks | Ka/Ks | Length/bp | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
bZIP2-bZIP43 | MA | 0.117946 | 0.165607 | 0.712204 | 960 | bZIP67-bZIP1 | MA | 0.097071 | 0.323816 | 0.299772 | 1 152 | |
bZIP3-bZIP44 | MA | 0.0130427 | 0.0128818 | 1.01249 | 489 | bZIP70-bZIP19 | MA | 0.0142327 | 0.0409637 | 0.347448 | 1 332 | |
bZIP10-bZIP38 | MA | 0.100549 | 0.140421 | 0.716056 | 846 | bZIP73-bZIP14 | MA | 0.0547414 | 0.0672358 | 0.81417 | 702 | |
bZIP10-bZIP112 | MA | 0.11451 | 0.521399 | 0.219622 | 879 | bZIP76-bZIP36 | MA | 0.110057 | 0.324559 | 0.339097 | 564 | |
bZIP11-bZIP37 | MA | 0.0942089 | 0.0981423 | 0.959922 | 957 | bZIP79-bZIP104 | MA | 0.0904191 | 0.339624 | 0.266233 | 462 | |
bZIP13-bZIP76 | MA | 0.104919 | 0.30191 | 0.347518 | 564 | bZIP87-bZIP81 | MA | 0.317343 | 0.931453 | 0.340696 | 1 065 | |
bZIP13-bZIP109 | MA | 0.101853 | 0.290082 | 0.351118 | 564 | bZIP92-bZIP51 | MA | 0.015582 | 0.0313318 | 0.497324 | 903 | |
bZIP15-bZIP54 | MA | 0.105643 | 0.321516 | 0.328579 | 972 | bZIP98-bZIP52 | MA | 0.0483138 | 0.0459249 | 1.05202 | 1 023 | |
bZIP15-bZIP55 | MA | 0.156553 | 0.426652 | 0.366934 | 1 197 | bZIP100-bZIP80 | MA | 0.0367017 | 0.113648 | 0.322942 | 1 086 | |
bZIP16-bZIP80 | MA | 0.0682639 | 0.322732 | 0.211519 | 1 128 | bZIP101-bZIP83 | MA | 0.0497949 | 0.0973565 | 0.51147 | 1 368 | |
bZIP16-bZIP100 | MA | 0.0627594 | 0.322994 | 0.194305 | 1 083 | bZIP105-bZIP60 | MA | 0.0758902 | 0.29116 | 0.260647 | 1 218 | |
bZIP36-bZIP109 | MA | 0.106955 | 0.312518 | 0.342235 | 564 | bZIP108-bZIP53 | MA | 0.0113524 | 0.0549189 | 0.206712 | 1 002 | |
bZIP45-bZIP20 | MA | 0.0126196 | 0.0519384 | 0.242973 | 435 | bZIP114-bZIP26 | MA | 0.0106575 | 0.0442045 | 0.241095 | 846 | |
bZIP46-bZIP24 | MA | 0.0182878 | 0.0429762 | 0.425534 | 1 533 | bZIP115-bZIP81 | MA | 0.242357 | 0.752788 | 0.321946 | 1 068 | |
bZIP47-bZIP23 | MA | 0.018861 | 0.0298436 | 0.631996 | 993 | bZIP115-bZIP82 | MA | 0.16807 | 0.619685 | 0.271218 | 1 308 | |
bZIP48-bZIP21 | MA | 0.0890243 | 0.194441 | 0.457848 | 663 | bZIP118-bZIP85 | MA | 0.114442 | 0.317447 | 0.360506 | 894 | |
bZIP50-bZIP95 | MA | 0.119225 | 0.411079 | 0.29003 | 843 | bZIP118-bZIP103 | MA | 0.0895535 | 0.261122 | 0.342957 | 885 | |
bZIP61-bZIP91 | MA | 0.168025 | 0.327658 | 0.512807 | 771 | bZIP119-bZIP32 | MA | 0.0231439 | 0.0836963 | 0.276523 | 996 |
Table 2 Replication mode of PqbZIPs for large-scale replication events
Sequence | Method | Ka | Ks | Ka/Ks | Length/bp | Sequence | Method | Ka | Ks | Ka/Ks | Length/bp | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
bZIP2-bZIP43 | MA | 0.117946 | 0.165607 | 0.712204 | 960 | bZIP67-bZIP1 | MA | 0.097071 | 0.323816 | 0.299772 | 1 152 | |
bZIP3-bZIP44 | MA | 0.0130427 | 0.0128818 | 1.01249 | 489 | bZIP70-bZIP19 | MA | 0.0142327 | 0.0409637 | 0.347448 | 1 332 | |
bZIP10-bZIP38 | MA | 0.100549 | 0.140421 | 0.716056 | 846 | bZIP73-bZIP14 | MA | 0.0547414 | 0.0672358 | 0.81417 | 702 | |
bZIP10-bZIP112 | MA | 0.11451 | 0.521399 | 0.219622 | 879 | bZIP76-bZIP36 | MA | 0.110057 | 0.324559 | 0.339097 | 564 | |
bZIP11-bZIP37 | MA | 0.0942089 | 0.0981423 | 0.959922 | 957 | bZIP79-bZIP104 | MA | 0.0904191 | 0.339624 | 0.266233 | 462 | |
bZIP13-bZIP76 | MA | 0.104919 | 0.30191 | 0.347518 | 564 | bZIP87-bZIP81 | MA | 0.317343 | 0.931453 | 0.340696 | 1 065 | |
bZIP13-bZIP109 | MA | 0.101853 | 0.290082 | 0.351118 | 564 | bZIP92-bZIP51 | MA | 0.015582 | 0.0313318 | 0.497324 | 903 | |
bZIP15-bZIP54 | MA | 0.105643 | 0.321516 | 0.328579 | 972 | bZIP98-bZIP52 | MA | 0.0483138 | 0.0459249 | 1.05202 | 1 023 | |
bZIP15-bZIP55 | MA | 0.156553 | 0.426652 | 0.366934 | 1 197 | bZIP100-bZIP80 | MA | 0.0367017 | 0.113648 | 0.322942 | 1 086 | |
bZIP16-bZIP80 | MA | 0.0682639 | 0.322732 | 0.211519 | 1 128 | bZIP101-bZIP83 | MA | 0.0497949 | 0.0973565 | 0.51147 | 1 368 | |
bZIP16-bZIP100 | MA | 0.0627594 | 0.322994 | 0.194305 | 1 083 | bZIP105-bZIP60 | MA | 0.0758902 | 0.29116 | 0.260647 | 1 218 | |
bZIP36-bZIP109 | MA | 0.106955 | 0.312518 | 0.342235 | 564 | bZIP108-bZIP53 | MA | 0.0113524 | 0.0549189 | 0.206712 | 1 002 | |
bZIP45-bZIP20 | MA | 0.0126196 | 0.0519384 | 0.242973 | 435 | bZIP114-bZIP26 | MA | 0.0106575 | 0.0442045 | 0.241095 | 846 | |
bZIP46-bZIP24 | MA | 0.0182878 | 0.0429762 | 0.425534 | 1 533 | bZIP115-bZIP81 | MA | 0.242357 | 0.752788 | 0.321946 | 1 068 | |
bZIP47-bZIP23 | MA | 0.018861 | 0.0298436 | 0.631996 | 993 | bZIP115-bZIP82 | MA | 0.16807 | 0.619685 | 0.271218 | 1 308 | |
bZIP48-bZIP21 | MA | 0.0890243 | 0.194441 | 0.457848 | 663 | bZIP118-bZIP85 | MA | 0.114442 | 0.317447 | 0.360506 | 894 | |
bZIP50-bZIP95 | MA | 0.119225 | 0.411079 | 0.29003 | 843 | bZIP118-bZIP103 | MA | 0.0895535 | 0.261122 | 0.342957 | 885 | |
bZIP61-bZIP91 | MA | 0.168025 | 0.327658 | 0.512807 | 771 | bZIP119-bZIP32 | MA | 0.0231439 | 0.0836963 | 0.276523 | 996 |
Fig. 5 Homology analysis of bZIPs between P. quinquefoli-us and Panax ginseng as well as P. quinquefolius and Panax notoginseng The gray lines on the background indicate collinear blocks in the genomes of P. quinquefolius and other plants; the green line highlights the bZIP gene pair of homologous P. quinquefolius
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