Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members
Abstract
:1. Introduction
2. Results
2.1. Characteristics of the Chloroplast Genome
2.2. Relative Synonymous Codon Usage (RSCU)
2.3. RNA Editing Sites
2.4. Repeat Analysis
2.4.1. Long Repeats
2.4.2. Simple Sequence Repeats
2.5. Sequence Divergence
2.6. Boundary between LSC/SSC and IRs
2.7. Divergence of Protein-Coding Gene Sequences
2.8. Heatmap
2.9. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. Library Construction
4.3. De Novo Genome Sequencing
4.4. Genome Assembly and Annotation
4.5. Sequence Analysis
4.6. Repeat Analysis in the Chloroplast Genome
4.7. Sequence Divergence and Boundary
4.8. Characterization of the Substitution Rate
4.9. Heatmap
4.10. Phylogenetic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Feature | P. acaciae | P. curviflorus |
---|---|---|
Genome size (bp) | 120,181 | 121,086 |
IRA (bp) | 22,323 | 22,476 |
IRB (bp) | 22,323 | 22,476 |
LSC (bp) | 69,497 | 69,947 |
SSC (bp) | 6038 | 6187 |
Total No of Genes | 106 | 108 |
Total No of Unique Genes | 92 | 92 |
rRNA | 4 | 4 |
tRNA | 25 | 25 |
Protein-Coding genes | 63 | 63 |
A% | 31.50 | 31.34 |
T (U) % | 31.93 | 31.89 |
G% | 17.97 | 18.12 |
C % | 18.59 | 18.65 |
%GC | 36.6 | 36.8 |
Gene | Strand | Location | Exon I (bp) | Intron I (bp) | Exon II (bp) | Intron II (bp) | Exon III (bp) |
---|---|---|---|---|---|---|---|
atpF | - | LSC | 145 | 801 | 401 | ||
ycf3 | - | LSC | 124 | 762 | 230 | 768 | 153 |
clpP | - | LSC | 71 | 767 | 294 | 675 | 229 |
petB | + | LSC | 6 | 814 | 642 | ||
rps12 | - | IRB | 56 | 515 | 229 | ||
+ | IRA | 229 | 515 | 56 | |||
rpl2 | - | IRB | 391 | 654 | 431 | ||
rpl16 | - | LSC | 303 | 486 | 9 | ||
petD | + | LSC | 8 | 743 | 484 | ||
trnL-UAA | + | LSC | 35 | 299 | 55 | ||
trnA-UGC | - | IRA | 55 | 342 | 39 | ||
+ | IRB | 39 | 342 | 55 |
Gene | Strand | Location | Exon I (bp) | Intron I (bp) | Exon II (bp) | Intron II (bp) | Exon III (bp) |
---|---|---|---|---|---|---|---|
atpF | - | LSC | 145 | 792 | 410 | ||
rpoC1 | - | LSC | 432 | 830 | 1617 | ||
ycf3 | - | LSC | 124 | 743 | 230 | 772 | 153 |
clpP | - | LSC | 71 | 752 | 294 | 524 | 229 |
rpl2 | - | IRB | 391 | 654 | 440 | ||
rps12 | - | IRB | 56 | 507 | 229 | ||
+ | IRA | 229 | 507 | 56 | |||
rpl16 | - | LSC | 9 | 893 | 81 | ||
petB | + | LSC | 6 | 864 | 642 | ||
trnL-UAA | + | LSC | 35 | 290 | 55 | ||
trnA-UGC | - | IRA | 55 | 350 | 37 | ||
+ | IRB | 37 | 350 | 55 |
SSR Type | Repeat Unit | Plicosepalus acacia | Plicosepalus curviflorus | Scurrula chingii | Taxillus chinensis | Loranthus europaeus | Dendrophthoe pentandra | Nuytsia floribunda | Elytranthe albida |
---|---|---|---|---|---|---|---|---|---|
Mono | A | 67 | 62 | 59 | 49 | 44 | 50 | 47 | 60 |
C | 2 | 2 | 4 | 7 | 6 | 6 | 3 | 6 | |
G | 1 | 0 | 2 | 2 | 2 | 0 | 3 | 2 | |
T | 69 | 70 | 87 | 86 | 67 | 78 | 69 | 87 | |
Di | AG/CT | 1 | 1 | 0 | 0 | 0 | 1 | 1 | 0 |
AT/AT | 10 | 6 | 13 | 6 | 7 | 5 | 12 | 3 | |
Tri | AAG/CTT | 2 | 2 | 2 | 2 | 2 | 2 | 0 | 0 |
AAT/ATT | 4 | 1 | 1 | 1 | 1 | 3 | 2 | 1 | |
ATC/ATG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | |
Tetra | AAAG/CTTT | 3 | 3 | 1 | 1 | 2 | 2 | 0 | 3 |
AAAT/ATTT | 4 | 2 | 1 | 0 | 4 | 5 | 3 | 1 | |
ACAG/CTGT | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | |
AGGG/CCCT | 0 | 2 | 2 | 0 | 2 | 2 | 0 | 0 | |
AAGT/ACTT | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
AATT/AATT | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | |
AATC/ATTG | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | |
AAAC/GTTT | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
AACC/GGTT | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
AGAT/ATCT | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | |
AATG/ATTC | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | |
Penta | AAAAT/ATTTT | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
AATAT/ATATT | 0 | 3 | 0 | 1 | 2 | 0 | 0 | 0 | |
Total | 164 | 155 | 175 | 157 | 143 | 155 | 142 | 169 |
Order | Family | Accession Number | Organism |
---|---|---|---|
Santalales | Loranthaceae | NC_053563 | Scurrula chingii (W.C.Cheng) H.S.Kiu |
MN080717 | Taxillus chinensis (DC.) Danser | ||
MN080718.1 | Helixanthera parasitica Lour. | ||
MT987630 | Loranthus europaeus Jacq. | ||
MT987635.1 | Loranthus pseudo-odoratus Lingelsh. | ||
NC_039376 | Macrosolen cochinchinensis (Lour.) Tiegh. | ||
NC_045107 | Dendrophthoe pentandra (L.) Miq. | ||
NC_045108 | Elytranthe albida (Blume) Blume | ||
NC_058837 | Taxillus pseudochinensis (Yamam.) Danser | ||
NC_058840 | Taxillus tsaii S.T.Chiu | ||
NC_058859 | Cecarria obtusifolia (Merr.) Barlow | ||
NC_058862.1 | Loranthus guizhouensis H.S.Kiu | ||
NC_058868 | Moquiniella rubra (A.Spreng.) Balle | ||
NC_058869 | Nuytsia floribunda (Labill.) R.Br. ex G.Don | ||
NC_058858.1 | Loranthus delavayi Tiegh. | ||
Santalaceae | NC_027960 | Osyris alba L. | |
Schoepfiaceae | NC_034228 | Schoepfia jasminodora Siebold & Zucc. | |
Viscaceae | KT003925.1 | Viscum album L. | |
NC_027829 | Viscum minimum Harv. | ||
Erythropalaceae | NC_036759.1 | Erythropalum scandens Blume | |
Lamiales | Orobanchaceae | NC_001568.1 | Epifagus virginiana (L.) Barton |
Solanales | Solanaceae | NC_001879 | Nicotiana tabacum L. |
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AL-Juhani, W.; Al Thagafi, N.T.; Al-Qthanin, R.N. Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. Plants 2022, 11, 1869. https://doi.org/10.3390/plants11141869
AL-Juhani W, Al Thagafi NT, Al-Qthanin RN. Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. Plants. 2022; 11(14):1869. https://doi.org/10.3390/plants11141869
Chicago/Turabian StyleAL-Juhani, Widad, Noha T. Al Thagafi, and Rahmah N. Al-Qthanin. 2022. "Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members" Plants 11, no. 14: 1869. https://doi.org/10.3390/plants11141869