Origin and Fates of TERT Gene Copies in Polyploid Plants
Abstract
:1. Introduction
2. Results
2.1. Number of TERT Variants in Nicotiana Polyploids as a Case Study
2.2. Origin of TERT Genes in Polyploids with the Ancestral N. sylvestris Donor Genome
2.2.1. Suaveolentes
2.2.2. Repandae
2.2.3. Nicotianae
2.3. Origin of the TERT Gene in Polyploid Sections Polydicliae, Rusticae and Undulatae
2.3.1. Polydicliae
2.3.2. Undulatae and Rusticae
2.4. Expression of TERT Variants in Nicotiana Polyploids
2.5. In Silico Analysis of N. sylvestris Genome Assembly Illustrates a Possible Evolutionary Scenario and the Origin of Subsequent Multiple TERT Loci
2.6. Genomic TERT Loci Analysis Defines Ancestral Synteny within Flowering Plants
2.7. The Occurrence of TERT Homologs in Model Species Illustrates a Possible Origin of TERT Variants
3. Discussion
4. Materials and Methods
4.1. Isolation of Plant Material, Genomic DNA and RNA
4.2. PCR Amplification of TERT Sequence Variants
4.3. Quantitative PCR and RT–qPCR
4.4. In Silico Identification of TERT Variants in Nicotiana Species
4.5. Analysis of Gene Synteny of the TERT Locus within Angiosperms
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
BLASTn | Basic local alignment search tool, nucleotide to nucleotide |
LTR | Long terminal repeat |
MtATPO | Mitochondrial ATP synthase subunit delta |
NGS | Next-generation sequencing |
qPCR | Quantitative PCR |
SNP | Single nucleotide polymorphism |
SRA | Short read archive |
TERT | Telomerase reverse transcriptase |
WGD | Whole-genome duplication |
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Allopolyploids | GeneBank Accessions | Sequence Similarity [%] | Analyzed Region 1 | |||
---|---|---|---|---|---|---|
Maternal Parent | Paternal Parent | |||||
SUAVEOLENTES | N. alata | N. noctiflora2 | N. syl. C var. | N. syl. D var. | ||
N. benthamiana | NbS000104 | 96.3 | n.a. | 97.5 | n.a. | exon 4 to 5 |
27g0116.1 | n.a. | 96.1 | 97.6 | 93.4 | exons 10, 11, 12 | |
REPANDAE | N. syl. C var. | N. syl. D var. | N. obtusifolia | |||
N. repanda | MG242402 1 | 95.9 | 91.6 | 97.4 | exon 9 | |
MG242403 1 | 97.9 | 92.4 | 96.4 | exon 9 | ||
N. stocktonii | MG242407 1 | 95.6 | 91.7 | 97.6 | exon 9 | |
MG242408 1 | 98.6 | 93.1 | 97.0 | exon 9 | ||
N. nesophila | MG242405 1 | 95.2 | 91.6 | 97.0 | exon 9 | |
MG242406 1 | 98.5 | 92.9 | 96.9 | exon 9 | ||
N. nudicaulis | MG242409 1 | 98.6 | 94.3 | 94.4 | exon 10 to 12 | |
MG545647 1 | 92.8 | 94.8 | 91.6 | exon 10 to 12 | ||
MG242410 1 | 94.2 | 93.3 | 96.3 | exon 10 to 12 | ||
POLYDICLIAE | N. obtusifolia | N. attenuata | ||||
MG242422 1 | 94.3 | 99.3 | exon 4 to 5 | |||
N. clevelandii | var1 2 | 97.3 | 98.9 | exon 9 2 | ||
var2 2 | 99.2 | 97.3 | exon 9 2 | |||
N. quadrivalvis | MG242423 1 | 94.9 | 98.6 | exon 4 to 5 | ||
ARENTSII | N. undulata | N. wigandiodes | ||||
N. arentsii | MG242418 1 | 99.5 | 98.4 | exon 9 | ||
MG242419 1 | 98.8 | 99.8 | exon 9 | |||
RUSTICA | N. paniculata | N. undulata | ||||
N. rustica | MG242413 1 | 100.0 | 98.2 | exon 9 | ||
MG242414 1 | 98.2 | 99.8 | exon 9 |
Species/Genome Dataset Accession | Total No. of TERT Reads | Expected Genome Coverage (Depth) | No. of Detected TERT Variants | Read Counts Corresponding to Known TERT Variants | Ratio of TERT Variants in Genome | ||
---|---|---|---|---|---|---|---|
N. tabacum SRX338107 | 1259 | 35× | 3 | NtTERT_Cs | NtTERT_D | NtTERT_Ct | 1:1:1 |
425 | 424 | 410 | |||||
N. sylvestris ERX248848 | 644 | 26× | 2 | NsTERT_C | NsTERT_D | 1:1 | |
332 | 312 | ||||||
N. tomentosiformis ERX248865 | 203 | 15× | 1 | NtomTERT | - | ||
203 | |||||||
N. benthamiana (raw data from [39]) | 286 | 20× | 1 | NbenTERT | - | ||
286 |
N. sylvestris Accession | Ct (±SD) | ∆Ct (C-C1/2×) | ∆Ct (C-D) | C:D Ratio | ||
---|---|---|---|---|---|---|
NsTERT_C | NsTERT_C 1/2× (Control) | NsTERT_D | ||||
A04750326 | 16.41 (±0.036) | 16.91 (±0.085) | 16.41 (±0.065) | −0.5 | 0.00 | 1:1 |
934750005 | 16.65 (±0.052) | 17.12 (±0.043) | 16.59 (±0.049) | −0.47 | 0.06 | 1:1 |
ITB626 | 17.65 (±0.067) | 18.12 (±0.051) | 17.66 (±0.035) | −0.47 | −0.01 | 1:1 |
TW136 | 17.25 (±0.02) | 17.68 (±0.015) | 17.13 (±0.043) | −0.43 | 0.12 | 1:1 |
Ducrettet 101-268 | 17.31 (±0.023) | 17.95 (±0.063) | 17.26 (±0.08) | −0.64 | 0.05 | 1:1 |
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Fajkus, P.; Peška, V.; Fajkus, J.; Sýkorová, E. Origin and Fates of TERT Gene Copies in Polyploid Plants. Int. J. Mol. Sci. 2021, 22, 1783. https://doi.org/10.3390/ijms22041783
Fajkus P, Peška V, Fajkus J, Sýkorová E. Origin and Fates of TERT Gene Copies in Polyploid Plants. International Journal of Molecular Sciences. 2021; 22(4):1783. https://doi.org/10.3390/ijms22041783
Chicago/Turabian StyleFajkus, Petr, Vratislav Peška, Jiří Fajkus, and Eva Sýkorová. 2021. "Origin and Fates of TERT Gene Copies in Polyploid Plants" International Journal of Molecular Sciences 22, no. 4: 1783. https://doi.org/10.3390/ijms22041783