Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies

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...

Mô tả đầy đủ

Đã lưu trong:
Chi tiết về thư mục
Tác giả chính: Hoàng, Thị Như Phương
Định dạng: Journal article
Ngôn ngữ:English
Được phát hành: 2022
Những chủ đề:
Spirodela polyrhiza, duckweeds, multicolor FISH, optical map, cytogenetic map, Oxford Nanopore sequencing, syntenous regions.
Truy cập trực tuyến:http://scholar.dlu.edu.vn/handle/123456789/1026
Các nhãn: Thêm thẻ
Không có thẻ, Là người đầu tiên thẻ bản ghi này!
Thư viện lưu trữ: Thư viện Trường Đại học Đà Lạt
id oai:scholar.dlu.edu.vn:123456789-1026
record_format dspace
institution Thư viện Trường Đại học Đà Lạt
collection Thư viện số
language English
topic Spirodela polyrhiza, duckweeds, multicolor FISH, optical map, cytogenetic map, Oxford Nanopore sequencing, syntenous regions.
spellingShingle Spirodela polyrhiza, duckweeds, multicolor FISH, optical map, cytogenetic map, Oxford Nanopore sequencing, syntenous regions.
Hoàng, Thị Như Phương
Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
description 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.
format Journal article
author Hoàng, Thị Như Phương
author_facet Hoàng, Thị Như Phương
author_sort Hoàng, Thị Như Phương
title Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
title_short Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
title_full Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
title_fullStr Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
title_full_unstemmed Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
title_sort generating a high-confidence reference genome map of the greater duckweed by integration of cytogenomic, optical mapping, and oxford nanopore technologies
publishDate 2022
url http://scholar.dlu.edu.vn/handle/123456789/1026
_version_ 1768305920282984448
spelling oai:scholar.dlu.edu.vn:123456789-10262022-09-15T11:22:55Z Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies Hoàng, Thị Như Phương Spirodela polyrhiza, duckweeds, multicolor FISH, optical map, cytogenetic map, Oxford Nanopore sequencing, syntenous regions. 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. 96 670–684 2022-09-15T11:22:54Z 2022-09-15T11:22:54Z 2018 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter http://scholar.dlu.edu.vn/handle/123456789/1026 0.1111/tpj.14049 en The Plant Journal Abd El-Twab, M.H. and Kondo, K. (2012) Physical mapping of 5S and 45S rDNA in Chrysanthemum and related genera of the Anthemideae by FISH, and species relationships. J. Genet. 91(2), 245–249. Ali, H.B., Lysak, M.A. and Schubert, I. (2005) Chromosomal localization of rDNA in the Brassicaceae. Genome, 48(2), 341–346. https://doi.org/10. 1139/g04-116 Amborella Genome Project. (2013) The Amborella genome and the evolution of flowering plants. Science, 342(6165), 1241089. Appenroth, K.-J., Teller, S. and Horn, M. (1996) Photophysiology of turion formation and germination in Spirodela polyrhiza. Biol. Plant. 38(1), 95– 106. https://doi.org/10.1007/bf02879642. Appenroth, K.J., Crawford, D.J. and Les, D.H. (2015) After the genome sequencing of duckweed - how to proceed with research on the fastest growing angiosperm? Plant Biol. (Stuttg), 17(Suppl 1), 1–4. https://doi. org/10.1111/plb.12248. Appenroth, K.J., Sree, K.S., Bohm, V., Hammann, S., Vetter, W., Leiterer, M. and Jahreis, G. (2017) Nutritional value of duckweeds (Lemnaceae) as human food. Food Chem. 217, 266–273. https://doi.org/10.1016/j.foodche m.2016.08.116. Bog, M., Lautenschlager, U., Landrock, M.F., Landolt, E., Fuchs, F., Sree, K.S., Oberprieler, C. and Appenroth, K.J. (2015) Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP). Hydrobiologia, 749, 169–182. Cabrera, L.I., Salazar, G.A., Chase, M.W., Mayo, S.J., Bogner, J. and Davila, P. (2008) Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA. Am. J. Bot. 95(9), 1153–1165. https://doi.org/10.3732/ajb.0800073. Cao, H.X., Vu, G.T., Wang, W., Appenroth, K.J., Messing, J. and Schubert, I. (2016) The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. New Phytol. 209(1), 354–363. https://doi.org/10.1111/nph.13592. Chamala, S., Chanderbali, A.S., Der, J.P. et al. (2013) Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science, 342(6165), 1516–1517. https://doi.org/10.1126/science.1241130. Chang, S.B., Yang, T.J., Datema, E. et al. (2008) FISH mapping and molecular organization of the major repetitive sequences of tomato. Chromosome Res. 16(7), 919–933. https://doi.org/10.1007/s10577-008-1249-z. Chaudhuri, D., Majumder, A., Misra, A.K. and Bandyopadhyay, K. (2014) Cadmium removal by Lemna minor and Spirodela polyrhiza. Int. J. Phytoremediation, 16(7–12), 1119–1132. https://doi.org/10.1080/15226514. 2013.821446. Cui, W. and Cheng, J.J. (2015) Growing duckweed for biofuel production: a review. Plant Biol. (Stuttg), 17(Suppl 1), 16–23. https://doi.org/10. 1111/plb.12216. Cusimano, N., Bogner, J., Mayo, S.J., Boyce, P.C., Wong, S.Y., Hesse, M., Hetterscheid, W.L., Keating, R.C. and French, J.C. (2011) Relationships within the Araceae: comparison of morphological patterns with molecular phylogenies. Am. J. Bot. 98(4), 654–668. https://doi.org/10.3732/ajb. 1000158. Ellinghaus, D., Kurtz, S. and Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9, 18. Gilchrist, C.A., Turner, S.D., Riley, M.F., Petri, W.A. Jr and Hewlett, E.L. (2015) Whole-genome sequencing in outbreak analysis. Clin. Microbiol. Rev. 28(3), 541–563. https://doi.org/10.1128/CMR.00075-13. Goswami, C., Majumder, A., Misra, A.K. and Bandyopadhyay, K. (2014) Arsenic uptake by Lemna minor in hydroponic system. Int. J. Phytoremediation, 16(7–12), 1221–1227. https://doi.org/10.1080/15226514.2013. 821452 Gottlob- McHugh, S.G., Levesque, M., MacKenzie, K., Olson, M., Yarosh, O. and Johnson, D.A. (1990) Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants. Genome, 33(4), 486–494. Heslop-Harrison, J.S., Harrison, G.E. and Leitch, I.J. (1992) Reprobing of DNA:DNA in situ hybridization preparations. Trends Genet. 8(11), 372– 373. Hoang, P.T.N. and Schubert, I. (2017). Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Chromosoma, 126(6), 729–739. https://d oi.org/10.1007/s00412-017-0636-7 Ijdo, J.W., Wells, R.A., Baldini, A. and Reeders, S.T. (1991) Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. Nucleic Acids Res. 19(17), 4780. Kobayashi, T. (2014) Ribosomal RNA gene repeats, their stability and cellular senescence. Proc Jpn Acad Ser B Phys Biol Sci. 90(4), 119–129. Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C. and Salzberg, S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5(2), R12. Kuzoff, R.K., Sweere, J.A., Soltis, D.E., Soltis, P.S. and Zimmer, E.A. (1998) The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15(3), 251–263. Lam, E., Appenroth, K.J., Michael, T., Mori, K. and Fakhoorian, T. (2014) Duckweed in bloom: the 2nd International Conference on Duckweed Research and Applications heralds the return of a plant model for plant biology. Plant Mol. Biol. 84(6), 737–742. https://doi.org/10.1007/s11103- 013-0162-9 Les, D.H., Crawford, D.J., Landolt, E., Gabel, J.D. and Kimball, R.T. (2002) Phylogeny and systematics of Lemnaceae, the Duckweed family. Syst. Bot. 27(2), 221–240.

Những quyển sách tương tự