Phylogenetic Analysis of Rare Crepis Species of the Crimean Flora (C. purpurea (Willd.) M. Bieb. and C. callicephala Juz.) Through Plastid Genome Reconstruction
5 affiliations
- 1Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- 2Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- 3Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- 4N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences, 127276 Moscow, Russia
- 5Institute of Fundamental and Applied Agrobiotechnologies, Siberian State University of Engineering and Biotechnology, 630039 Novosibirsk, Russia
Abstract
One of the largest genera within the Cichorieae tribe of the Asteraceae family is Crepis, comprising ∼200 species. The diversity of numerous local forms is of interest for adaptation studies. There are two rare closely related species within the Lagoseris clade of the genus Crepis which occupy highly divergent habitats—C. callicephala Juz. and C. purpurea (Willd.) M. Bieb.—both occurring in the Crimean Peninsula. The habitats differ in environmental conditions and are isolated by location and altitude, restricting opportunities for gamete exchange. The species are similar morphologically but demonstrate different phenological patterns, representing a notable natural model for investigating how isolation and habitat conditions may shape genetic differentiation and local adaptation. We sequenced the total DNA of C. callicephala and C. purpurea. Relying on both short-read and long-read data, we assembled plastid genomes of these species and reconstructed the phylogeny of the subtribe Crepidinae. The assembled plastid genomes are 149,980 bp (C. callicephala) and 150,007 bp (C. purpurea), and the two species were recovered as a closely related pair on a long common branch within the sampled Crepidinae. We also noted an unusual structural rearrangement in the rbcL–psaI locus shared by the studied accessions of both species, affecting the accD gene (encoding the β-carboxyltransferase subunit of acetyl-CoA carboxylase), which has not been reported in other members of Cichorioideae. Together with the shifts in the inverted-repeat boundaries, these features provide molecular data relevant to the taxonomic status and relationship of C. callicephala and C. purpurea.
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BibTeX
@article{emirsaliev2026phylogenetic,
title = {{Phylogenetic Analysis of Rare Crepis Species of the Crimean Flora (C. purpurea (Willd.) M. Bieb. and C. callicephala Juz.) Through Plastid Genome Reconstruction}},
author = {Asan O. Emirsaliev and Dmitry A. Afonnikov and Irina V. Mitrofanova and Elena A. Salina and Alex V. Kochetov},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219446},
url = {https://www.mdpi.com/1422-0067/27/21/9446},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Phylogenetic Analysis of Rare Crepis Species of the Crimean Flora (C. purpurea (Willd.) M. Bieb. and C. callicephala Juz.) Through Plastid Genome Reconstruction
AU - Asan O. Emirsaliev
AU - Dmitry A. Afonnikov
AU - Irina V. Mitrofanova
AU - Elena A. Salina
AU - Alex V. Kochetov
PY - 2026
DA - 2026/10/23
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219446
UR - https://www.mdpi.com/1422-0067/27/21/9446
AB - One of the largest genera within the Cichorieae tribe of the Asteraceae family is Crepis, comprising ∼200 species. The diversity of numerous local forms is of interest for adaptation studies. There are two rare closely related species within the Lagoseris clade of the genus Crepis which occupy highly divergent habitats—C. callicephala Juz. and C. purpurea (Willd.) M. Bieb.—both occurring in the Crimean Peninsula. The habitats differ in environmental conditions and are isolated by location and altitude, restricting opportunities for gamete exchange. The species are similar morphologically but demonstrate different phenological patterns, representing a notable natural model for investigating how isolation and habitat conditions may shape genetic differentiation and local adaptation. We sequenced the total DNA of C. callicephala and C. purpurea. Relying on both short-read and long-read data, we assembled plastid genomes of these species and reconstructed the phylogeny of the subtribe Crepidinae. The assembled plastid genomes are 149,980 bp (C. callicephala) and 150,007 bp (C. purpurea), and the two species were recovered as a closely related pair on a long common branch within the sampled Crepidinae. We also noted an unusual structural rearrangement in the rbcL–psaI locus shared by the studied accessions of both species, affecting the accD gene (encoding the β-carboxyltransferase subunit of acetyl-CoA carboxylase), which has not been reported in other members of Cichorioideae. Together with the shifts in the inverted-repeat boundaries, these features provide molecular data relevant to the taxonomic status and relationship of C. callicephala and C. purpurea.
SN - 1422-0067
ER -