Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives
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© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Castanea, a prominent genus within the Fagaceae family, thrives across the expansive
woodlands of eastern North America, Europe, and Asia, holding considerable ecological
and economic significance. Among the invaluable forest resources, chestnuts play a pivotal
role by providing both nourishment and wood products. Furthermore, they assume the
status of keystone species due to their indispensable ecological functions in afforestation
and the provision of crucial ecosystem services. The genomes of C. mollissima and C. sativa,
estimated to be around 800 Mb in size, add to the remarkable genetic complexity of these
species. We utilized the powerful Python module jcvi to conduct a thorough synteny
analysis, focusing on the Chinese and European chestnut genomes. To detect structural
variants between these genomes, we employed SyRI (Synteny and Rearrangement
Identifier). Additionally, TBtools was utilized to visually illustrate the syntenic genes
across different genomes. Our inves...tigation involved a comprehensive synteny analysis
of the Chinese chestnut genome and the Sariaslama cultivar of the European chestnut.
Encouragingly, we observed a strong overall synteny between these genomes, indicating
significant conservation. To enhance the accuracy and completeness of the genome
assemblies, we employed Pacbio sequencing technology, which contributed to the highquality
results obtained for both the European and Chinese chestnut genomes.
Keywords:
genome sequencing / chinese chestnut / european chestnut / synteny analysisSource:
4th Belgrade Bioinformatics Conference, 2023, 4, 72-72Publisher:
- Belgrade : Institute of molecular genetics and genetic engineering
Funding / projects:
- The study was funded by Akdeniz University Scientific Research Projects Coordination Unit. Grant number: FBA- 2023-6237.
Note:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
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Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Tevfik Uncu, Ali AU - Aydin Akbudak, M. PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2011 AB - Castanea, a prominent genus within the Fagaceae family, thrives across the expansive woodlands of eastern North America, Europe, and Asia, holding considerable ecological and economic significance. Among the invaluable forest resources, chestnuts play a pivotal role by providing both nourishment and wood products. Furthermore, they assume the status of keystone species due to their indispensable ecological functions in afforestation and the provision of crucial ecosystem services. The genomes of C. mollissima and C. sativa, estimated to be around 800 Mb in size, add to the remarkable genetic complexity of these species. We utilized the powerful Python module jcvi to conduct a thorough synteny analysis, focusing on the Chinese and European chestnut genomes. To detect structural variants between these genomes, we employed SyRI (Synteny and Rearrangement Identifier). Additionally, TBtools was utilized to visually illustrate the syntenic genes across different genomes. Our investigation involved a comprehensive synteny analysis of the Chinese chestnut genome and the Sariaslama cultivar of the European chestnut. Encouragingly, we observed a strong overall synteny between these genomes, indicating significant conservation. To enhance the accuracy and completeness of the genome assemblies, we employed Pacbio sequencing technology, which contributed to the highquality results obtained for both the European and Chinese chestnut genomes. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives EP - 72 SP - 72 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2011 ER -
@conference{ author = "Tevfik Uncu, Ali and Aydin Akbudak, M.", year = "2023", abstract = "Castanea, a prominent genus within the Fagaceae family, thrives across the expansive woodlands of eastern North America, Europe, and Asia, holding considerable ecological and economic significance. Among the invaluable forest resources, chestnuts play a pivotal role by providing both nourishment and wood products. Furthermore, they assume the status of keystone species due to their indispensable ecological functions in afforestation and the provision of crucial ecosystem services. The genomes of C. mollissima and C. sativa, estimated to be around 800 Mb in size, add to the remarkable genetic complexity of these species. We utilized the powerful Python module jcvi to conduct a thorough synteny analysis, focusing on the Chinese and European chestnut genomes. To detect structural variants between these genomes, we employed SyRI (Synteny and Rearrangement Identifier). Additionally, TBtools was utilized to visually illustrate the syntenic genes across different genomes. Our investigation involved a comprehensive synteny analysis of the Chinese chestnut genome and the Sariaslama cultivar of the European chestnut. Encouragingly, we observed a strong overall synteny between these genomes, indicating significant conservation. To enhance the accuracy and completeness of the genome assemblies, we employed Pacbio sequencing technology, which contributed to the highquality results obtained for both the European and Chinese chestnut genomes.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives", pages = "72-72", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2011" }
Tevfik Uncu, A.,& Aydin Akbudak, M.. (2023). Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 72-72. https://hdl.handle.net/21.15107/rcub_imagine_2011
Tevfik Uncu A, Aydin Akbudak M. Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives. in 4th Belgrade Bioinformatics Conference. 2023;4:72-72. https://hdl.handle.net/21.15107/rcub_imagine_2011 .
Tevfik Uncu, Ali, Aydin Akbudak, M., "Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives" in 4th Belgrade Bioinformatics Conference, 4 (2023):72-72, https://hdl.handle.net/21.15107/rcub_imagine_2011 .