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Scobeyeva VA, Artyushin IV, Krinitsina AA, Nikitin PA, Antipin MI, Kuptsov SV, Belenikin MS, Omelchenko DO, Logacheva MD, Konorov EA, Samoilov AE, Speranskaya AS. Gene Loss, Pseudogenization in Plastomes of Genus Allium ( Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions. Front Genet 2021; 12:674783. [PMID: 34306019 PMCID: PMC8296844 DOI: 10.3389/fgene.2021.674783] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus—Allium—is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes’ annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the “normal” or “pseudo” state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
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Affiliation(s)
- Victoria A Scobeyeva
- Department of Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasiya A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim I Antipin
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei V Kuptsov
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim S Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, Moscow, Russia
| | - Maria D Logacheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgenii A Konorov
- Laboratory of Animal Genetics, Vavilov Institute of General Genetics, Russian Academy of Science (RAS), Moscow, Russia
| | - Andrey E Samoilov
- Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna S Speranskaya
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
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Zhang W, Wang H, Dong J, Zhang T, Xiao H. Comparative chloroplast genomes and phylogenetic analysis of Aquilegia. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11412. [PMID: 33854846 PMCID: PMC8027367 DOI: 10.1002/aps3.11412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
PREMISE Aquilegia is an ideal taxon for studying the evolution of adaptive radiation. Current phylogenies of Aquilegia based on different molecular markers are inconsistent, and therefore a clear and accurate phylogeny remains uncertain. Analyzing the chloroplast genome, with its simple structure and low recombination rate, may help solve this problem. METHODS Next-generation sequencing data were generated or downloaded for Aquilegia species, enabling their chloroplast genomes to be assembled. The assemblies were used to estimate the genome characteristics and infer the phylogeny of Aquilegia. RESULTS In this study, chloroplast genome sequences were assembled for Aquilegia species distributed across Asia, North America, and Europe. Three of the genes analyzed (petG, rpl36, and atpB) were shown to be under positive selection and may be related to adaptation. The phylogenetic tree of Aquilegia showed that its member species formed two clades with high support, North American and European species, with the Asian species being paraphyletic; A. parviflora and A. amurensis clustered with the North American species, while the remaining Asian species were found in the European clade. In addition, A. oxysepala var. kansuensis should be considered as a separate species rather than a variety. DISCUSSION The complete chloroplast genomes of these Aquilegia species provide new insights into the reconstruction of the phylogeny of related species and contribute to the further study of this genus.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Jianhua Dong
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of EducationNortheast Normal UniversityChangchun130024China
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