Chinese Bulletin of Botany ›› 2020, Vol. 55 ›› Issue (3): 287-298.DOI: 10.11983/CBB19105
• EXPERIMENTAL COMMUNICATIONS • Previous Articles Next Articles
Yang Peng1,Yingjuan Su2,3,*(),Ting Wang1,*(
)
Received:
2019-06-06
Accepted:
2020-03-24
Online:
2020-05-01
Published:
2020-07-06
Contact:
Yingjuan Su,Ting Wang
Yang Peng, Yingjuan Su, Ting Wang. Intron Loss and Molecular Evolution Rate of rpoC1 in Ferns[J]. Chinese Bulletin of Botany, 2020, 55(3): 287-298.
Family name | Species | GenBank accession number | Length (bp) |
---|---|---|---|
Aspleniaceae | Asplenium pekinense | KY427331 | 152479 |
As. prolongatum | KY427332 | 151115 | |
Hymenasplenium unilaterale | KY427350 | 151723 | |
Athyriaceae | Athyrium anisopterum | NC_035738 | 151284 |
At. opacum | KY427335 | 150979 | |
At. sheareri | KY427330 | 151068 | |
At. sinense | KY427333 | 151319 | |
Deparia lancea | KY427338 | 151011 | |
De. pycnosora | KY427339 | 151126 | |
De. viridifrons | KY427340 | 150939 | |
Diplazium bellum | KY427343 | 151601 | |
Di. dilatatum | KY427344 | 151114 | |
Di. dushanense | KY427345 | 150179 | |
Di. striatum | KY427346 | 150779 | |
Di. unilobum | KY427347 | 127840 | |
Blechnaceae | Austroblechnum melanocaulon | KY427334 | 150202 |
Woodwardia unigemmata | NC_028543 | 153717 | |
Cibotiaceae | Cibotium barometz | MH105066 | 166027 |
Cyatheaceae | Alsophila podophylla | MG262389 | 166151 |
Al. spinulosa | NC_012818 | 156661 | |
Cystopteridaceae | Cystopteris chinensis | KY427337 | 151269 |
Family name | Species | GenBank accession number | Length (bp) |
Dennstaedtiaceae | Pteridium aquilinum | NC_014348 | 152362 |
Diplaziopsidaceae | Diplaziopsis cavaleriana | KY427341 | 151934 |
Dip. javanica | KY427342 | 151496 | |
Homalosorus pycnocarpos | KY427349 | 152159 | |
Dryopteridaceae | Cyrtomium devexiscapulae | NC_028542 | 151684 |
C. falcatum | NC_028705 | 151628 | |
C. fortunei | MG913607 | 151699 | |
Dryopteris decipiens | KY427348 | 150987 | |
Dr. fragrans | KX418656 | 151978 | |
Equisetaceae | Equisetum arvense | NC_014699 | 133309 |
E. hyemale | NC_020146 | 131760 | |
Hymenophyllaceae | Callistopteris apiifolia | MH265125 | 144918 |
Hymenophyllum holochilum | MH265124 | 142214 | |
Vandenboschia speciosa | NC_041000 | 146874 | |
Hypodematiaceae | Hypodematium crenatum | KY427351 | 149794 |
Lygodiaceae | Lygodium japonicum | NC_022136 | 157260 |
L. microphyllum | NC_039378 | 158891 | |
Marattiaceae | Angiopteris angustifolia | NC_026300 | 153596 |
An. evecta | NC_008829 | 153901 | |
Marsileaceae | Marsilea crenata | NC_022137 | 151628 |
Pilularia americana | KY863504 | 153076 | |
Onocleaceae | Matteuccia struthiopteris | KY427353 | 151003 |
Onoclea sensibilis | KY427354 | 148395 | |
Ophioglossaceae | Botrychium ternatum | KM817789 | 139127 |
Helminthostachys zeylanica | KM817788 | 145120 | |
Mankyua chejuensis | NC_017006 | 146221 | |
Osmundaceae | Osmundastrum cinnamomeum | NC_024157 | 142812 |
Polypodiaceae | Lepisorus clathratus | NC_035739 | 156998 |
Polypodium glycyrrhiza | KP136832 | 129223 | |
Psilotaceae | Psilotum nudum | NC_003386 | 138829 |
Pteridaceae | Adiantum shastense | MG432483 | 150414 |
Ceratopteris richardii | KM052729 | 148444 | |
Myriopteris lindheimeri | NC_014592 | 155770 | |
Rhachidosoraceae | Rhachidosorus consimilis | KY427356 | 152642 |
Schizaeaceae | Schizaea elegans | KX258660 | 156603 |
S. pectinata | KX258661 | 156392 | |
Thelypteridaceae | Ampelopteris prolifera | KY427329 | 151772 |
Christella appendiculata | NC_035842 | 151571 | |
Macrothelypteris torresiana | KY427352 | 151130 | |
Pseudophegopteris aurita | KY427355 | 149917 | |
Stegnogramma sagittifolia | KY427357 | 151132 | |
Woodsiaceae | Woodsia macrochlaena | KY427358 | 150987 |
W. polystichoides | KY427359 | 150685 |
Table 1 Plant materials used in this study and GenBank accession numbers of chloroplast genome sequences
Family name | Species | GenBank accession number | Length (bp) |
---|---|---|---|
Aspleniaceae | Asplenium pekinense | KY427331 | 152479 |
As. prolongatum | KY427332 | 151115 | |
Hymenasplenium unilaterale | KY427350 | 151723 | |
Athyriaceae | Athyrium anisopterum | NC_035738 | 151284 |
At. opacum | KY427335 | 150979 | |
At. sheareri | KY427330 | 151068 | |
At. sinense | KY427333 | 151319 | |
Deparia lancea | KY427338 | 151011 | |
De. pycnosora | KY427339 | 151126 | |
De. viridifrons | KY427340 | 150939 | |
Diplazium bellum | KY427343 | 151601 | |
Di. dilatatum | KY427344 | 151114 | |
Di. dushanense | KY427345 | 150179 | |
Di. striatum | KY427346 | 150779 | |
Di. unilobum | KY427347 | 127840 | |
Blechnaceae | Austroblechnum melanocaulon | KY427334 | 150202 |
Woodwardia unigemmata | NC_028543 | 153717 | |
Cibotiaceae | Cibotium barometz | MH105066 | 166027 |
Cyatheaceae | Alsophila podophylla | MG262389 | 166151 |
Al. spinulosa | NC_012818 | 156661 | |
Cystopteridaceae | Cystopteris chinensis | KY427337 | 151269 |
Family name | Species | GenBank accession number | Length (bp) |
Dennstaedtiaceae | Pteridium aquilinum | NC_014348 | 152362 |
Diplaziopsidaceae | Diplaziopsis cavaleriana | KY427341 | 151934 |
Dip. javanica | KY427342 | 151496 | |
Homalosorus pycnocarpos | KY427349 | 152159 | |
Dryopteridaceae | Cyrtomium devexiscapulae | NC_028542 | 151684 |
C. falcatum | NC_028705 | 151628 | |
C. fortunei | MG913607 | 151699 | |
Dryopteris decipiens | KY427348 | 150987 | |
Dr. fragrans | KX418656 | 151978 | |
Equisetaceae | Equisetum arvense | NC_014699 | 133309 |
E. hyemale | NC_020146 | 131760 | |
Hymenophyllaceae | Callistopteris apiifolia | MH265125 | 144918 |
Hymenophyllum holochilum | MH265124 | 142214 | |
Vandenboschia speciosa | NC_041000 | 146874 | |
Hypodematiaceae | Hypodematium crenatum | KY427351 | 149794 |
Lygodiaceae | Lygodium japonicum | NC_022136 | 157260 |
L. microphyllum | NC_039378 | 158891 | |
Marattiaceae | Angiopteris angustifolia | NC_026300 | 153596 |
An. evecta | NC_008829 | 153901 | |
Marsileaceae | Marsilea crenata | NC_022137 | 151628 |
Pilularia americana | KY863504 | 153076 | |
Onocleaceae | Matteuccia struthiopteris | KY427353 | 151003 |
Onoclea sensibilis | KY427354 | 148395 | |
Ophioglossaceae | Botrychium ternatum | KM817789 | 139127 |
Helminthostachys zeylanica | KM817788 | 145120 | |
Mankyua chejuensis | NC_017006 | 146221 | |
Osmundaceae | Osmundastrum cinnamomeum | NC_024157 | 142812 |
Polypodiaceae | Lepisorus clathratus | NC_035739 | 156998 |
Polypodium glycyrrhiza | KP136832 | 129223 | |
Psilotaceae | Psilotum nudum | NC_003386 | 138829 |
Pteridaceae | Adiantum shastense | MG432483 | 150414 |
Ceratopteris richardii | KM052729 | 148444 | |
Myriopteris lindheimeri | NC_014592 | 155770 | |
Rhachidosoraceae | Rhachidosorus consimilis | KY427356 | 152642 |
Schizaeaceae | Schizaea elegans | KX258660 | 156603 |
S. pectinata | KX258661 | 156392 | |
Thelypteridaceae | Ampelopteris prolifera | KY427329 | 151772 |
Christella appendiculata | NC_035842 | 151571 | |
Macrothelypteris torresiana | KY427352 | 151130 | |
Pseudophegopteris aurita | KY427355 | 149917 | |
Stegnogramma sagittifolia | KY427357 | 151132 | |
Woodsiaceae | Woodsia macrochlaena | KY427358 | 150987 |
W. polystichoides | KY427359 | 150685 |
Et | Ev | trsv/trst | trst | trsv | dN | dS | ω | |
---|---|---|---|---|---|---|---|---|
Lygodium | 0.014 | 0.004 | 0.118 | 0.579 | 0.007 | 0.022 | 0.147 | 0.144 |
Other ferns | 0.022 | 0.005 | 0.096 | 0.088 | 0.010 | 0.045 | 0.201 | 0.256 |
P value | 1.000 | 1.000 | 1.000 | 0.008 | 0.036 | 0.000 | 0.517 | 1.000 |
Mann-Whitney | 0.834 | 0.778 | 0.362 | 0.834 | 0.778 | 0.502 | 0.923 | 0.316 |
Table 2 Evolution rate test of rpoC1 coding sequences (CDS) of Lygodium and other ferns
Et | Ev | trsv/trst | trst | trsv | dN | dS | ω | |
---|---|---|---|---|---|---|---|---|
Lygodium | 0.014 | 0.004 | 0.118 | 0.579 | 0.007 | 0.022 | 0.147 | 0.144 |
Other ferns | 0.022 | 0.005 | 0.096 | 0.088 | 0.010 | 0.045 | 0.201 | 0.256 |
P value | 1.000 | 1.000 | 1.000 | 0.008 | 0.036 | 0.000 | 0.517 | 1.000 |
Mann-Whitney | 0.834 | 0.778 | 0.362 | 0.834 | 0.778 | 0.502 | 0.923 | 0.316 |
Amino acid sites | |
---|---|
Positive selection sites | 156, 184, 568 |
Negative selection sites | 1-3, 6-12, 14-21, 23-26, 28-32, 35-37, 39-42, 44-54, 56, 58-63, 66-74, 76, 79-82, 84, 86-102, 104-107, 109-128, 130-136, 138, 139, 141-144, 147-155, 158-173, 180-181, 183, 186-191, 193-195, 197-198, 200-208, 211, 213-218, 223, 225, 228-230, 232-235, 237, 241-244, 246-247, 249-258, 260-276, 278-291, 294-296, 298-301, 303-315, 318-337, 339-344, 346-368, 370-391, 393-400, 402-411, 413-414, 416-417, 419-434, 436-437, 439-440, 442, 444-445, 447-449, 453-455, 457-480, 482-492, 494-499, 501-526, 528-538, 540-550, 553-556, 558-561, 566-567, 575, 577, 579, 582-583, 586-588, 590-591, 593, 597-600, 603-613, 620, 622, 625-626, 628, 630, 632-635, 639, 642-644, 646, 648-649, 654, 660, 663-668, 671-674, 676, 677, 679-682, 687-689, 694, 697, 710 |
Table 3 Positive and negative selection sites of rpoC1
Amino acid sites | |
---|---|
Positive selection sites | 156, 184, 568 |
Negative selection sites | 1-3, 6-12, 14-21, 23-26, 28-32, 35-37, 39-42, 44-54, 56, 58-63, 66-74, 76, 79-82, 84, 86-102, 104-107, 109-128, 130-136, 138, 139, 141-144, 147-155, 158-173, 180-181, 183, 186-191, 193-195, 197-198, 200-208, 211, 213-218, 223, 225, 228-230, 232-235, 237, 241-244, 246-247, 249-258, 260-276, 278-291, 294-296, 298-301, 303-315, 318-337, 339-344, 346-368, 370-391, 393-400, 402-411, 413-414, 416-417, 419-434, 436-437, 439-440, 442, 444-445, 447-449, 453-455, 457-480, 482-492, 494-499, 501-526, 528-538, 540-550, 553-556, 558-561, 566-567, 575, 577, 579, 582-583, 586-588, 590-591, 593, 597-600, 603-613, 620, 622, 625-626, 628, 630, 632-635, 639, 642-644, 646, 648-649, 654, 660, 663-668, 671-674, 676, 677, 679-682, 687-689, 694, 697, 710 |
Model | Np | ? | Parameter estimate | Positive selection sites | |
---|---|---|---|---|---|
Branch model | M0 | 128 | -33984.0181 | ω=0.18862 | Not allowed |
MA | 129 | -33971.0708 | ω1=0.19344, ω2=0.07154 | Not allowed | |
Site model | Model 1a (M1a) | 129 | -33025.1095 | P0=0.77581, ω0=0.09604 | Not allowed |
P1=0.22419, ω1=1.00000 | |||||
Model 2a (M2a) | 131 | -33003.8671 | P0=0.77323, ω0=0.09782 | 687P**, 697S** | |
P1=0.20583, ω1=1.00000 | 692S**, 700A* | ||||
P2=0.02094, ω2=2.53148 | |||||
Model 3 (M3) | 132 | -32770.6265 | P0=0.45915, ω0=0.02383 | None | |
P1=0.39593, ω1=0.23422 | |||||
P2=0.14492, ω2=0.91531 | |||||
Model 7 (M7) | 129 | -32768.3591 | P=0.36168, q=1.11178 | Not allowed | |
Model 8 (M8) | 131 | -32715.0671 | P0=0.95310, P=0.46388 | 578V*, 579Y*, 686S* | |
q=2.02806, P1=0.04690 | 687P**, 689T*, 692S** | ||||
ω=1.62513 | 693I*, 696T*, 697S**, 700A* | ||||
Model 8a (M8a) | 130 | -32735.2130 | P0=0.91188, P=0.48169 | None | |
q=2.38635, P1=0.08812 | |||||
ω=1.00000 | |||||
Branch-site model | Ma0 | 130 | -33025.1095 | P0=0.77581, P1=0.22419 | Not allowed |
P2a+P2b=0.00000, ω2=1.00000 | |||||
Ma1 | 131 | -33025.1095 | P0=0.77581, P1=0.22419 | None | |
P2a+P2b=0.00000, ω2=1.00000 |
Table 4 Parameters estimates and log-likelihood values of the rpoC1 gene under different models
Model | Np | ? | Parameter estimate | Positive selection sites | |
---|---|---|---|---|---|
Branch model | M0 | 128 | -33984.0181 | ω=0.18862 | Not allowed |
MA | 129 | -33971.0708 | ω1=0.19344, ω2=0.07154 | Not allowed | |
Site model | Model 1a (M1a) | 129 | -33025.1095 | P0=0.77581, ω0=0.09604 | Not allowed |
P1=0.22419, ω1=1.00000 | |||||
Model 2a (M2a) | 131 | -33003.8671 | P0=0.77323, ω0=0.09782 | 687P**, 697S** | |
P1=0.20583, ω1=1.00000 | 692S**, 700A* | ||||
P2=0.02094, ω2=2.53148 | |||||
Model 3 (M3) | 132 | -32770.6265 | P0=0.45915, ω0=0.02383 | None | |
P1=0.39593, ω1=0.23422 | |||||
P2=0.14492, ω2=0.91531 | |||||
Model 7 (M7) | 129 | -32768.3591 | P=0.36168, q=1.11178 | Not allowed | |
Model 8 (M8) | 131 | -32715.0671 | P0=0.95310, P=0.46388 | 578V*, 579Y*, 686S* | |
q=2.02806, P1=0.04690 | 687P**, 689T*, 692S** | ||||
ω=1.62513 | 693I*, 696T*, 697S**, 700A* | ||||
Model 8a (M8a) | 130 | -32735.2130 | P0=0.91188, P=0.48169 | None | |
q=2.38635, P1=0.08812 | |||||
ω=1.00000 | |||||
Branch-site model | Ma0 | 130 | -33025.1095 | P0=0.77581, P1=0.22419 | Not allowed |
P2a+P2b=0.00000, ω2=1.00000 | |||||
Ma1 | 131 | -33025.1095 | P0=0.77581, P1=0.22419 | None | |
P2a+P2b=0.00000, ω2=1.00000 |
Model comparison | Df. | 2Δl | P value |
---|---|---|---|
M0 & MA | 1 | 25.8947 | 3.606×10-7 |
M1a & M2a | 2 | 42.4848 | 5.950×10-10 |
M0 & M3 | 4 | 2426.7832 | 0 |
M7 & M8 | 2 | 106.5838 | 0 |
M8a & M8 | 1 | 40.2917 | 2.187×10-10 |
M0 & MF | 125 | 169.4740 | 4.998×10-3 |
Table 5 Likelihood ratio test statistic (2Δ?) for different models in PAML4.9
Model comparison | Df. | 2Δl | P value |
---|---|---|---|
M0 & MA | 1 | 25.8947 | 3.606×10-7 |
M1a & M2a | 2 | 42.4848 | 5.950×10-10 |
M0 & M3 | 4 | 2426.7832 | 0 |
M7 & M8 | 2 | 106.5838 | 0 |
M8a & M8 | 1 | 40.2917 | 2.187×10-10 |
M0 & MF | 125 | 169.4740 | 4.998×10-3 |
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