Plant Genosystematics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 11474

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Department of Evolutionary Biochemistry, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
Interests: plant molecular phylogeny and systematics; genome evolution; biodiversity; phytoplanktonic metagenome
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Special Issue Information

Dear Colleagues,

“Genosystematics” is not a widely used term. It was introduced by Andrey Antonov [1] following Sisir Dutta's "DNA systematics" [2] to designate a scientific field, the task of which is to use data on the structure of information macromolecules (semantids) to recognize the systematic position and phylogeny of living organisms. Genosystematics started at the turn of the 50s and 60s of the last century in the works of Lee et al. [3] and the Belozersky team [4] on the elucidation of the kinship relationship between bacteria from the nucleotide composition of DNA. Some time later, the first works on the use of data on the proteins amino acid sequences for phylogenetic reconstructions appeared. A comparative analysis of globins led to the idea of using the number of amino acid substitutions in proteins to estimate the time of their divergence [5].

Over its sixty-year history, genosystematics has come a long way, absorbing the methodological innovations of molecular biology—from paper chromatography of nucleotide bases through DNA-DNA hybridization, isozyme, and immunological analysis to high-throughput sequencing of genomes of the second and now the third generation.

Genosystematics has changed the face of biological systematics and phylogenetics. At present, no research in these areas is possible without the involvement of genosystematic data, the results of which are reflected in global projects such as Tree of Life (http://tolweb.org) and International Barcode of Life (https://ibol.org). The progress of genosystematics is inextricably linked with the development of bioinformatics methods for the analysis of semantids based initially on Henning's cladistics, the large-scale implementation of which became possible due to the creation of extensive semantids databases, the development of computer technologies, and WWW network communication.

A significant number of genosystematic studies have been devoted to plants, leading to a revision of the concepts of phylogeny and taxonomy of many groups. However, the field for research in this area is still far from being closed. This is evidenced by at least the discovery through genome analysis of a new phylum within green plants in recent weeks [6].

In the current Special Issue, it is planned to publish original research, reviews, and short communications on the genosystematics of various groups of terrestrial plants and algae, as well as on methodological and bioinformatics developments in this area.

[1] Antonov, A.S. Genosystematics: from E. Chargaff and A.N. Belozersky to the present. Molecular Biology 2005, 39, 495–502.

[2] Dutta, S. K. (ed.) DNA Systematics v. I-II. CRC Press, Boca Raton, FL USA, 1986.  ISBN 13: 978-0-367-25137-6 (hbk); 13: 978-0-429-28628-5 (ebk).

[3] Lee, K. Y.; Wahl, R.; Barbu, E. Contenu en bases puriques et pyrimidiques des acides desoxyribonucléiques des bactéries. Ann. Inst. Pasteur 1956, 91, 212-224.

[4] Spirin A.S., Belozersky A.N., Shugayeva N.V., Vanyushin B.F. A study of species specificity with respect to nucleic acids in bacteria. Biochemistry (Moscow) 1957, 22, 699−707.

[5] Zuckerkandl, E.; Pauling, L. Molecular disease, evolution, and genetic heterogeneity. In Horizons in biochemistry eds. Kasha, M.; Pullman, B.; Academic Press, New York, USA, 1962; pp. 189–225.

[6] Li, L.; Wang, S.; Wang, H.; et al. The genome of Prasinoderma colonial unveils the existence of a third phylum within green plants. Nat. Ecol. Evol. 2020 4, 1220–1231. https://doi.org/10.1038/s41559-020-1221-7

Prof. Dr. Alex Troitsky
Guest Editor

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Keywords

  • plants
  • genosystematics
  • molecular phylogeny
  • systematics

Published Papers (4 papers)

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Research

56 pages, 17526 KiB  
Article
Calypogeia (Calypogeiaceae, Marchantiophyta) in Pacific Asia: Updates from Molecular Revision with Particular Attention to the Genus in North Indochina
by Vadim A. Bakalin, Yulia D. Maltseva, Frank Müller, Ksenia G. Klimova, Van Sinh Nguyen, Seung Se Choi and Aleksey V. Troitsky
Plants 2022, 11(7), 983; https://doi.org/10.3390/plants11070983 - 4 Apr 2022
Cited by 12 | Viewed by 2756
Abstract
Calypogeia is a genus in Pacific Asia that is difficult to classify taxonomically. These difficulties arise from (1) considering the presence of oil bodies as anatomical characters for taxonomic differentiation, (2) the wide occurrence of sibling, semicryptic and geographical vicariant taxa and (3) [...] Read more.
Calypogeia is a genus in Pacific Asia that is difficult to classify taxonomically. These difficulties arise from (1) considering the presence of oil bodies as anatomical characters for taxonomic differentiation, (2) the wide occurrence of sibling, semicryptic and geographical vicariant taxa and (3) the inevitable need to organize new datasets for molecular genetic revision of the genus. The present study uses an integrative approach, including molecular genetic, morphological, chorological and ecological methods, to understand the taxonomy of the genus in Amphi-Pacific Asia. As a result, a set of new-to-science taxa was revealed, and the suite of morphological features necessary for reliable discrimination of the taxa was revised. These results are based on the study of a large set of ‘fresh’ collections suitable for molecular analysis and morphological comparison and include data on oil bodies. The most basal branch in Calypogeia s.l. is segregated into a new genus, Asperifolia. Descriptions of the new taxa and the key to Calypogeia in Vietnam are provided. Full article
(This article belongs to the Special Issue Plant Genosystematics)
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18 pages, 2487 KiB  
Article
Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)
by Tahir Samigullin, Maria Logacheva, Elena Terentieva, Galina Degtjareva, Michael Pimenov and Carmen Valiejo-Roman
Plants 2022, 11(5), 709; https://doi.org/10.3390/plants11050709 - 7 Mar 2022
Cited by 6 | Viewed by 2508
Abstract
Based on the nrDNA ITS sequence data, the Tordylieae tribe is recognized as monophyletic with three major lineages: the subtribe Tordyliinae, the Cymbocarpum clade, and the Lefebvrea clade. Recent phylogenomic investigations showed incongruence between the nuclear and plastid genome evolution in the tribe. [...] Read more.
Based on the nrDNA ITS sequence data, the Tordylieae tribe is recognized as monophyletic with three major lineages: the subtribe Tordyliinae, the Cymbocarpum clade, and the Lefebvrea clade. Recent phylogenomic investigations showed incongruence between the nuclear and plastid genome evolution in the tribe. To assess phylogenetic relations and structure evolution of plastomes in Tordylieae, we generated eleven complete plastome sequences using the genome skimming approach and compared them with the available data from this tribe and close relatives. Newly assembled plastomes had lengths ranging from 141,148 to 150,103 base pairs and contained 122–127 genes, including 79–82 protein-coding genes, 35–37 tRNAs, and 8 rRNAs. We observed substantial differences in the inverted repeat length and gene content, accompanied by a complex picture of multiple JLA and JLB shifts. In concatenated phylogenetic analyses, Tordylieae plastomes formed at least three not closely related lineages with plastomes of the Lefebvrea clade as a sister group to plastomes from the Selineae tribe. The newly obtained data have increased our knowledge on the range of plastome variability in Apiaceae. Full article
(This article belongs to the Special Issue Plant Genosystematics)
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19 pages, 6894 KiB  
Article
Characterization of 15-cis-ζ-Carotene Isomerase Z-ISO in Cultivated and Wild Tomato Species Differing in Ripe Fruit Pigmentation
by Gleb I. Efremov, Anna V. Shchennikova and Elena Z. Kochieva
Plants 2021, 10(11), 2365; https://doi.org/10.3390/plants10112365 - 2 Nov 2021
Cited by 9 | Viewed by 2461
Abstract
Isomerization of 9,15,9′-tri-cis-ζ-carotene mediated by 15-cis-ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade (Solanum section Lycopersicon) comprises the cultivated tomato (Solanum lycopersicum) and 12 related [...] Read more.
Isomerization of 9,15,9′-tri-cis-ζ-carotene mediated by 15-cis-ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade (Solanum section Lycopersicon) comprises the cultivated tomato (Solanum lycopersicum) and 12 related wild species differing in fruit color and, thus, represents a good model for studying carotenogenesis in fleshy fruit. In this study, we identified homologous Z-ISO genes, including 5′-UTRs and promoter regions, in 12 S. lycopersicum cultivars and 5 wild tomato species (red-fruited Solanum pimpinellifolium, yellow-fruited Solanum cheesmaniae, and green-fruited Solanum chilense, Solanum habrochaites, and Solanum pennellii). Z-ISO homologs had a highly conserved structure, suggesting that Z-ISO performs a similar function in tomato species despite the difference in their fruit color. Z-ISO transcription levels positively correlated with the carotenoid content in ripe fruit of the tomatoes. An analysis of the Z-ISO promoter and 5′-UTR sequences revealed over 130 cis-regulatory elements involved in response to light, stresses, and hormones, and in the binding of transcription factors. Green- and red/yellow-fruited Solanum species differed in the number and position of cis-elements, indicating changes in the transcriptional regulation of Z-ISO expression during tomato evolution, which likely contribute to the difference in fruit color. Full article
(This article belongs to the Special Issue Plant Genosystematics)
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14 pages, 1918 KiB  
Article
Plant DNA Barcode as a Tool for Root Identification in Hypogea: The Case of the Etruscan Tombs of Tarquinia (Central Italy)
by Daniela Isola, Flavia Bartoli, Simone Langone, Simona Ceschin, Laura Zucconi and Giulia Caneva
Plants 2021, 10(6), 1138; https://doi.org/10.3390/plants10061138 - 3 Jun 2021
Cited by 10 | Viewed by 2865
Abstract
Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can [...] Read more.
Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can be taken against herbaceous plants lacking fast and reliable root identification methods that are useful to assess their dangerousness. In this study, we aimed to test the efficacy of DNA barcoding in identifying plant rootlets threatening the Etruscan tombs of the Necropolis of Tarquinia. As DNA barcode markers, we selected two sections of the genes rbcL and matK, the nuclear ribosomal internal transcribed spacer (nrITS), and the intergenic spacer psbA-trnH. All fourteen root samples were successfully sequenced and identified at species (92.9%) and genus level (7.01%) by GenBank matching and reference dataset implementation. Some eudicotyledons with taproots, such as Echium italicum L., Foeniculum vulgare Mill., and Reseda lutea L. subsp. lutea, showed a certain recurrence. Further investigations are needed to confirm this promising result, increasing the number of roots and enlarging the reference dataset with attention to meso-Mediterranean perennial herbaceous species. The finding of herbaceous plants roots at more than 3 m deep confirms their potential risk and underlines the importance of vegetation planning, monitoring, and management on archaeological sites. Full article
(This article belongs to the Special Issue Plant Genosystematics)
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