Conflicting Phylogenetic Signals between the Nuclear Ribosomal and Plastome DNA as Evidence for Hybrid Origin of the Tetraploid Member of Salicornia (Amaranthaceae s.l.)

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Tahir H. Samigullin^1,a*, Maria D. Logacheva^1,2, Galina V. Degtjareva^1,3, Dmitry D. Sokoloff⁴, Svetlana S. Beer⁵, and Carmen M. Valiejo-Roman¹

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia

²Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia

³Research and Educational Center – Botanical Garden of Peter I, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

⁴School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997820, Israel

⁵Private School “Obninsk Free School”, 249038 Obninsk, Russia

^* To whom correspondence should be addressed.

Received: July 8, 2025; Revised: October 6, 2025; Accepted: October 8, 2025

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Species of the genus Salicornia (Amaranthaceae s.l.) are globally distributed and highly salt-tolerant. They are used as food and for biofuel production. Formation of pure lines through self-pollination, combined with sporadic cross-pollination, polyploidy, high phenotypic plasticity, and a limited number of diagnostic characters, significantly complicates taxonomy of the genus. Salicornia (glassworts) is an evolutionarily young group, where the number of informative substitutions in the traditionally analyzed regions of nuclear and plastid DNA is insufficient to establish relationships between the species. The very concept of a species in this genus remains a subject of debate. To clarify relationships among the Eastern European species, we used high-throughput sequencing to determine sequences and perform phylogenetic analysis of the plastomes of 11 samples representing all major morphotypes of Eastern European glassworts. We also analyzed variability of the nuclear rDNA external transcribed spacer (nrETS). The sizes of the assembled plastomes ranged from 153,290 bp to 153,504 bp and exhibited a typical architecture with a large single-copy region (84,625-84,797 bp), a small single-copy region (18,818-18,870 bp), and two inverted repeats (24,898-24,908 bp). Comparison of phylogenetic trees reconstructed from all currently available plastome data and nrETS alignments of the same glasswort accessions revealed a discrepancy in the placement of the tetraploid S. procumbens subsp. pojarkovae and S. brachiata accessions, which show affinities to different lineages depending on the use of either plastid or nuclear (nrETS) data. Our results highlight the role of reticulate evolution in the genus Salicornia.

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KEY WORDS: plastome, nrETS DNA, phylogenetic signal conflict, polyploidy, hybridization, Salicornia

DOI: 10.1134/S0006297925602072

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