Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds
Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyr...
Đã lưu trong:
| Những tác giả chính: | , , , , , |
|---|---|
| Định dạng: | Journal article |
| Ngôn ngữ: | English |
| Được phát hành: |
Springer Berlin Heidelberg
2023
|
| Truy cập trực tuyến: | https://scholar.dlu.edu.vn/handle/123456789/3171 |
| 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:123456789-3171 |
|---|---|
| record_format |
dspace |
| institution |
Thư viện Trường Đại học Đà Lạt |
| collection |
Thư viện số |
| language |
English |
| description |
Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth
rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in
genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are
available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome
homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other
duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to
address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a).
Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are
not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity
between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of
oligo-probes to elucidate chromosome evolution across duckweed genera. |
| format |
Journal article |
| author |
Hoàng, Thị Như Phương Jean, Marie Rouillard Jiří, Macas Ivona, Kubalová Veit, Schubert Ingo, Schubert |
| spellingShingle |
Hoàng, Thị Như Phương Jean, Marie Rouillard Jiří, Macas Ivona, Kubalová Veit, Schubert Ingo, Schubert Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| author_facet |
Hoàng, Thị Như Phương Jean, Marie Rouillard Jiří, Macas Ivona, Kubalová Veit, Schubert Ingo, Schubert |
| author_sort |
Hoàng, Thị Như Phương |
| title |
Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| title_short |
Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| title_full |
Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| title_fullStr |
Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| title_full_unstemmed |
Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds |
| title_sort |
limitation of current probe design for oligo-cross-fish, exemplified by chromosome evolution studies in duckweeds |
| publisher |
Springer Berlin Heidelberg |
| publishDate |
2023 |
| url |
https://scholar.dlu.edu.vn/handle/123456789/3171 |
| _version_ |
1783866428379627520 |
| spelling |
oai:scholar.dlu.edu.vn:123456789-31712023-11-15T08:34:59Z Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds Hoàng, Thị Như Phương Jean, Marie Rouillard Jiří, Macas Ivona, Kubalová Veit, Schubert Ingo, Schubert Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera. 130 1 15-25 2023-11-15T08:34:52Z 2023-11-15T08:34:52Z 2021-03 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter https://scholar.dlu.edu.vn/handle/123456789/3171 10.1007/s00412-020-00749-2 en Chromosoma 1432-0886 Appenroth K-J, Teller S, Horn M (1996) Photophysiology of turion formation and germination inSpirodela polyrhiza. Biol Plant 38:95– 106. https://doi.org/10.1007/bf02879642 Aurich-Costa J, Zamechek L, Keenan P, Bradley S (2007) Oligo fluorescence in situ hybridization (oligo-fish), a new strategy for enumerating chromosomes in interphase nuclei. Fertil Steril 88:S86. https:// doi.org/10.1016/j.fertnstert.2007.07.287 Bog M, Sree KS, Fuchs J, Hoang PTN, Schubert I, Kuever J, Rabenstein A, Paolacci S, Jansen MAK, Appenroth KJ (2020) A taxonomic revision of Lemna sect. Uninerves (Lemnaceae). Taxon 69:56–66. https://doi.org/10.1002/tax.12188 Braz GT et al (2018) Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 208:513–523. https://doi.org/10.1534/genetics.117. 300344 Cao HX, Vu GT, Wang W, Appenroth KJ, Messing J, Schubert I (2016) The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. New Phytol 209:354–363. https://doi.org/10.1111/nph.13592 de Beukelaar MFA, Zeinstra GG, Mes JJ, Fischer ARH (2019) Duckweed as human food. The influence of meal context and information on duckweed acceptability of Dutch consumers. Food Qual Prefer 71:76–86. https://doi.org/10.1016/j.foodqual.2018.06.005 Han Y, Zhang T, Thammapichai P, Weng Y, Jiang J (2015) Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200:771–779. https://doi.org/10.1534/ genetics.115.177642 Harkess A,McLaughlin F, Bilkey N, Elliot K, Emenecker R, Mattoon E, Miller K, Czymme KK, Vierstra R,Meyers BC, Michael TP (2020) A new Spirodela polyrhiza genome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production. bioRxiv. https://doi.org/10.1101/2020. 01.23.909457 Hoang PTN (2019) Comparative cytology and cytogenomics for representative species of the five duckweed genera., Halle/S., Martin- Luther-Universität Halle-Wittenberg Hoang PTN, Fiebig A, Novák P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I (2020) Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci Rep 10:19230. https://doi.org/10.1038/s41598-020-75728-9 Hoang PTN, Schubert I (2017) Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Chromosoma 126:729–739. https://doi. org/10.1007/s00412-017-0636-7 Hoang PTN, Schubert V,Meister A, Fuchs J, Schubert I (2019) Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Sci Rep 9:3234. https://doi.org/10. 1038/s41598-019-39332-w Hoang PNT et al (2018) Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies. Plant J 96:670– 684. https://doi.org/10.1111/tpj.14049 Ijdo JW, Wells RA, Baldini A, Reeders ST (1991) Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. Nucleic Acids Res 19:4780 Jiang JM (2019) Fluorescent in situ hybridization in plants: recent developments and future directions. Chromosome Res 27:153-165. https://doi.org/10.1007/s10577-019-09607-z Springer Berlin Heidelberg |