Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. The Genome of U. pustulata
2.2. Pool-Seq Sequencing of 15 U. pustulata Populations
2.3. De Novo TE Prediction: Building a U. pustulata TE Consensus Library
2.4. Evaluation of TE Copy Insertion Frequencies across the Different U. pustulata Populations
2.5. Identification of TE Loci Significantly Differentiated between U. pustulata Ecotypes
2.6. Functional Characterization
2.7. Population Structure Based on Genome-Wide SNPs
3. Results
3.1. TE Landscape in U. pustulata
3.2. TE Variation across U. pustulata Populations
3.3. Variations of TE Frequencies between Ecotypes
3.4. Potential Functional Impact of TE Insertions
4. Discussion
4.1. The U. pustulata Mobilome
4.2. Ecotypic Differentiation Patterns of TE Insertions and Their Potential Functional Impact
4.3. Outlook and Future Perspectives
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Country | Population ID | Lat | Long | Elevation m a.s.l. | No. Paired-End Read # | Mean Read Length |
---|---|---|---|---|---|---|
Italy | IT1 | 40.7577 | 9.0794 | 176 | 29,162,770 | 99.3 |
IT2 | 40.7778 | 9.0546 | 297 | 28,279,628 | 99.3 | |
IT3 | 40.8503 | 9.1119 | 588 | 26,570,943 | 99.4 | |
IT4 | 40.8568 | 9.1340 | 842 | 31,720,828 | 99.4 | |
IT5 | 40.8573 | 9.1642 | 1125 | 31,755,901 | 99.4 | |
IT6 | 40.8524 | 9.1732 | 1303 | 32,064,853 | 99.4 | |
Spain 1 | ESii1 | 40.2028 | −5.2334 | 706 | 26,758,269 | 141.8 |
ESii2 | 40.2069 | −5.2327 | 887 | 24,295,101 | 141.7 | |
ESii3 | 40.2116 | −5.2337 | 1082 | 29,236,274 | 141.9 | |
ESii4 | 40.2183 | −5.2335 | 1258 | 33,333,561 | 141.6 | |
ESii5 | 40.2253 | −5.2375 | 1480 | 24,672,545 | 141.7 | |
ESii6 | 40.2322 | −5.2389 | 1699 | 26,690,508 | 141.5 | |
Spain 2 | ESi1 | 39.9946 | −4.8679 | 477 | 28,862,057 | 99.5 |
ESi2 | 40.2899 | −4.9927 | 859 | 37,303,042 | 99.5 | |
ESi3 | 40.3230 | −5.0173 | 1417 | 35,351,050 | 99.5 |
A. Summary of Class I and II TE elements found in the U. pustulata genome. | |||||||||||
Class | Total Length | No. Copies | No. Full Length Copies | Median Identity 1 | Median Length | ||||||
Class II | 1,146,170 | 1863 | 156 | 91.4 | 657.9 | ||||||
Class I | 5,118,614 | 2902 | 465 | 90.3 | 1162.5 | ||||||
unknown | 731,643 | 1191 | 83 | 88.1 | 323.4 | ||||||
B. Summary of TE elements subdivided into superfamilies for the U. pustulata genome. | |||||||||||
Class | Order | Superfamily | No. Elements | Total Length | No. Copies | No. Full Length Copies | Median Identity 1 | Median Length | |||
Class II | DHX | Helitron_01 | 7 | 553,513 | 680 | 23 | 88.7 | 498.6 | |||
DTA | HAT | 1 | 24,206 | 80 | 4 | 89.98 | 186.5 | ||||
DTB | PiggyBac | 1 | 12,236 | 10 | 4 | 95.3 | 1481.0 | ||||
DTT | Tc1Mar | 4 | 104,574 | 139 | 28 | 89.6 | 1029.4 | ||||
DTX | TIR | 18 | 380,415 | 824 | 86 | 92.0 | 648.2 | ||||
DXX | MITE | 4 | 71,226 | 130 | 11 | 93.0 | 521.0 | ||||
Class I | RII + RIX | LINE | 5 | 317,234 | 155 | 33 | 94.0 | 923.1 | |||
RLC | Copia | 25 | 1,333,809 | 865 | 166 | 92.0 | 1350.2 | ||||
RLG | Gypsy | 23 | 2,904,582 | 1296 | 215 | 89.8 | 1246.0 | ||||
RLX | LTR | 15 | 538,504 | 550 | 46 | 86.2 | 942.6 | ||||
RXX | LARD | 1 | 20,415 | 25 | 1 | 816.6 | 383.0 | ||||
RXX | TRIM | 1 | 4070 | 11 | 4 | 96.8 | 126.0 | ||||
No | Unknown | 14 | 731,643 | 1191 | 83 | 88.1 | 323.4 | ||||
total | 119 | 6,996,427 | 5956 | 704 | 147.1 | 743.0 |
A. TE copy insertion in 15 populations of U. pustulata (min. physical coverage: 16×). | ||
TE Family | Copy No. | % |
Copia | 62 | 34.1 |
TIR | 31 | 17.0 |
Unknown | 23 | 12.6 |
Helitron | 22 | 12.1 |
Gypsy | 16 | 8.8 |
LTR | 10 | 5.5 |
MITE | 8 | 4.4 |
LARD | 5 | 2.7 |
TC1Mar | 2 | 1.1 |
HAT | 1 | 0.5 |
LINE | 1 | 0.5 |
Piggybac | 1 | 0.5 |
B. Polymorphic TE copy insertion in populations. | ||
TE Family | Copy No. | % |
Copia | 49 | 43.0 |
TIR | 22 | 19.3 |
Unknown | 13 | 11.4 |
Helitron | 10 | 8.8 |
Gypsy | 5 | 4.4 |
LTR | 5 | 4.4 |
MITE | 5 | 4.4 |
LARD | 1 | 0.9 |
TC1Mar | 2 | 1.8 |
HAT | 1 | 0.9 |
Piggybac | 1 | 0.9 |
C. hdTEs between U. pustulata ecotypes. | ||
TE Family | Copy No. | % |
Copia | 16 | 57.1 |
TIR | 4 | 14.3 |
Helitron | 3 | 10.7 |
Unknown | 3 | 10.7 |
MITE | 1 | 3.6 |
PiggyBac | 1 | 3.6 |
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Dal Grande, F.; Jamilloux, V.; Choisne, N.; Calchera, A.; Rolshausen, G.; Petersen, M.; Schulz, M.; Nilsson, M.A.; Schmitt, I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. Biology 2022, 11, 24. https://doi.org/10.3390/biology11010024
Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. Biology. 2022; 11(1):24. https://doi.org/10.3390/biology11010024
Chicago/Turabian StyleDal Grande, Francesco, Véronique Jamilloux, Nathalie Choisne, Anjuli Calchera, Gregor Rolshausen, Malte Petersen, Meike Schulz, Maria A. Nilsson, and Imke Schmitt. 2022. "Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation" Biology 11, no. 1: 24. https://doi.org/10.3390/biology11010024