Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae)
The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.865958/full |
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| author | Olga Yu. Yurkevich Tatiana E. Samatadze Tatiana E. Samatadze Inessa Yu. Selyutina Natalia A. Suprun Svetlana N. Suslina Svyatoslav A. Zoshchuk Alexandra V. Amosova Olga V. Muravenko |
| author_facet | Olga Yu. Yurkevich Tatiana E. Samatadze Tatiana E. Samatadze Inessa Yu. Selyutina Natalia A. Suprun Svetlana N. Suslina Svyatoslav A. Zoshchuk Alexandra V. Amosova Olga V. Muravenko |
| author_sort | Olga Yu. Yurkevich |
| collection | DOAJ |
| description | The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20–24% (Class I) and about 2–2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5–10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia. |
| first_indexed | 2024-12-11T10:52:44Z |
| format | Article |
| id | doaj.art-d3db645c06bc45979570cd67b367b298 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T10:52:44Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d3db645c06bc45979570cd67b367b2982022-12-22T01:10:13ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-04-011310.3389/fpls.2022.865958865958Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae)Olga Yu. Yurkevich0Tatiana E. Samatadze1Tatiana E. Samatadze2Inessa Yu. Selyutina3Natalia A. Suprun4Svetlana N. Suslina5Svyatoslav A. Zoshchuk6Alexandra V. Amosova7Olga V. Muravenko8Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaPeoples’ Friendship University of Russia, Moscow, RussiaCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaCentral Volgograd Regional Botanical Garden, Volgograd, RussiaPeoples’ Friendship University of Russia, Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaThe section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20–24% (Class I) and about 2–2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5–10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.https://www.frontiersin.org/articles/10.3389/fpls.2022.865958/fullnext-generation sequencing (NGS)Hedysarum L.repeatometandem DNAs5S rDNAFISH analysis |
| spellingShingle | Olga Yu. Yurkevich Tatiana E. Samatadze Tatiana E. Samatadze Inessa Yu. Selyutina Natalia A. Suprun Svetlana N. Suslina Svyatoslav A. Zoshchuk Alexandra V. Amosova Olga V. Muravenko Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) Frontiers in Plant Science next-generation sequencing (NGS) Hedysarum L. repeatome tandem DNAs 5S rDNA FISH analysis |
| title | Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) |
| title_full | Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) |
| title_fullStr | Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) |
| title_full_unstemmed | Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) |
| title_short | Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae) |
| title_sort | integration of genomic and cytogenetic data on tandem dnas for analyzing the genome diversity within the genus hedysarum l fabaceae |
| topic | next-generation sequencing (NGS) Hedysarum L. repeatome tandem DNAs 5S rDNA FISH analysis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.865958/full |
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