Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yi...
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| Định dạng: | Journal article |
| Ngôn ngữ: | English |
| Được phát hành: |
2022
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| Những chủ đề: | |
| Truy cập trực tuyến: | http://scholar.dlu.edu.vn/handle/123456789/1026 |
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| Thư viện lưu trữ: | Thư viện Trường Đại học Đà Lạt |
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| Tóm tắt: | Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable
crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through
vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference
maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules,
and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes
(BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual
chromosome models. We validated both maps further to resolve these differences and addressed whether
they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential
multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that
were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford
Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome
models. We found no major structural rearrangements between these seven clones, identified seven chimeric
pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza
genome map with high contiguity was produced with the ON sequence data and genome-wide synteny
analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work
generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the
complementarity of independent approaches to produce whole-genome assemblies in the absence of a
genetic map. |
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