Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

Samigullin, Tahir H.; Logacheva, Maria D.; Terentieva, E.I.; Degtjareva, Galina V.; Пименов, М. Г.; Valiejo‐Roman, Carmen M.

doi:10.3390/plants11050709

Cited by 7 publications

(6 citation statements)

References 99 publications

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“…Whole plastome phylogenetic analysis shows that H. sosnowskyi is grouped with other species of the genus and with related monotypic genera Symphyoloma and Mandenovia (Figure S3). The same was inferred from the analysis of nuclear markers (Logacheva et al, 2010); the results are also congruent with those of a recent plastid phylogenomic study that included species of Heracleum other than H. sosnowskyi (Samigullin et al, 2022).…”

Section: Genome Assembly and Annotationsupporting

confidence: 88%

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications

Schelkunov,

Shtratnikova,

Klepikova

et al. 2023

The Plant Journal

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SUMMARYHeracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome‐scale assembly of Sosnowsky's hogweed genome. Genomic analysis revealed an unusually high number of genes (55106) in the hogweed genome, in contrast to the 25–35 thousand found in most plants. However, we did not find any traces of recent whole‐genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates on tandem duplications as a main reason for this increase. We performed a genome‐wide search of the genes of the FC biosynthesis pathway and surveyed their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.

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Section: Genome Assembly and Annotationsupporting

confidence: 88%

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications

Schelkunov,

Shtratnikova,

Klepikova

et al. 2023

The Plant Journal

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show abstract

“…Whole plastome phylogenetic analysis shows that H. sosnowskyi is grouped with other species of the genus and with related monotypic genera Symphyoloma and Mandenovia (Supplementary Figure S3). The same was inferred from the analysis of nuclear markers (Logacheva et al, 2010); the results are also congruent with those of a plastid phylogenomic study that included species of Heracleum other than H. sosnowskyi (Samigullin et al, 2022).…”

Section: Genome Assembly and Annotationsupporting

confidence: 83%

The genome of the toxic invasive speciesHeracleum sosnowskyicarries an increased number of genes despite absence of recent whole-genome duplications

Schelkunov

Shtratnikova

Klepikova

et al. 2023

Preprint

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Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value that are used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of the Sosnowsky's hogweed genome. Genomic analysis revealed an unusually high number of genes (55 206) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.

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“…Plastomes have been widely used in studying the phylogeny of Apiaceae, Ranunculaceae Juss., Saxifragaceae Juss., Allium L., Liliaceae Juss., etc. [27][28][29][30][31][32][33][34][35][36][37]. However, there has been no study on the phylogeny of Seseli based on plastomes and therefore there is ample opportunity to investigate phylogenetic and taxonomic issues of Seseli using plastomes.…”

Section: Introductionmentioning

confidence: 99%

The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

et al. 2022

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Background The genus Seseli L., which consists of 125–140 species distributed in the Old World from western Europe and northwestern Africa to China and Japan, is one of the largest and most taxonomically difficult genera of Apiaceae Lindl. Although several previous studies have been conducted on Seseli based on limited morphological characteristics and molecular fragments, a robust and comprehensive phylogeny of Seseli remains elusive. Plastomes provide abundant genetic information and have been widely used in studying plant phylogeny and evolution. Consequently, we newly generated the complete plastomes of eleven Seseli taxa. We combined plastome data and morphological characteristics to investigate the phylogeny of Seseli. Results In our study, we observed that the genome length, gene numbers, IR/SC borders, and repeat composition of the eleven Seseli plastomes were variable. Several appropriate mutation hotspot regions may be developed as candidate DNA barcodes for evolution, phylogeny, and species identification of Seseli. The phylogenetic results identified that Seseli was not a monophyletic group. Moreover, the eleven newly sequenced Seseli taxa did not cluster with S. tortuosum (the type species of Seseli, belonging to the tribe Selineae), where S. delavayi clustered with Eriocycla belonging to the tribe Echinophoreae and the other ten belonged to Selineae. The comparative plastome and morphological characteristics analyses confirmed the reliability of the phylogenetic analyses and implied the complex evolution of Seseli. Conclusion Combining molecular and morphological data is efficient and useful for studying the phylogeny of Seseli. We suggest that “a narrow sense” of Seseli will be meaningful for further study and the current taxonomic system of Seseli needs to be revised. In summary, our study can provide new insights into the phylogenetic relationships and taxonomic framework of Seseli.

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Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

Cited by 7 publications

References 99 publications

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications

The genome of the toxic invasive speciesHeracleum sosnowskyicarries an increased number of genes despite absence of recent whole-genome duplications

The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

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