Next Article in Journal
From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding
Next Article in Special Issue
Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome
Previous Article in Journal
The Potential for Trypsin Inhibitor Expression in Leaves to Convey Herbivory Deterrence in Soybean
Previous Article in Special Issue
Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 14
Issue 4
10.3390/plants14040618
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Sixteen New Complete Plastid Genomes in the Tribe Loteae (Leguminosae): Structure and Phylogenetic Analysis

by
Tahir H. Samigullin
1,*,
Yury O. Kopylov-Guskov
2,3,
Olga V. Nikitina
2,
Anastasiya A. Krinitsina
2,
Svetlana V. Polevova
2 and
Tatiana E. Kramina
2
1
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
2
Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119234 Moscow, Russia
3
Faculty of Biology, Shenzhen MSU-BIT University, No. 1, International University Park Road, Dayun New Town, Longgang, Shenzhen 518172, China
*
Author to whom correspondence should be addressed.
Plants 2025, 14(4), 618; https://doi.org/10.3390/plants14040618
Submission received: 29 December 2024 / Revised: 5 February 2025 / Accepted: 14 February 2025 / Published: 18 February 2025
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)
Browse Figures
Versions Notes

Abstract

The tribe Loteae (Papilioniodeae-Leguminosae), according to plastid data, belongs to the Robinioid clade, which also includes the tribes Robinieae and Sesbanieae. The tribe Loteae contains 16 genera and about two hundred seventy-five species, of which the plastid genomes of five species have been studied to date. The main objectives of our study were to obtain new information on the plastid genome structure of the Loteae representatives in order to assess plastid genome variability and reconstruct phylogenetic relationships within the tribe Loteae. We performed sequencing, assembly, structural and phylogenetic analyses of the Loteae plastid genomes. All assembled Loteae plastomes showed a quadripartite structure with an overall length ranging from 150,069 to 152,206 bp and showed relative stability of inverted repeat borders. The Loteae plastomes demonstrated full collinearity; the most variable sites of the studied plastomes were found in petN-trnC and rps16-accD spacers from the LSC region and in the ycf1 gene within the SSC. All inferred relationships attained maximal support with the Hippocrepis lineage separated first, followed by Coronilla and Anthyllis; Lotus is a sister group to the clade Acmispon + Ornithopus. In this study, completely resolved relationships representing a backbone of plastid phylogeny were produced. The obtained results demonstrated that plastid genomes in the tribe Loteae are structurally conservative in contrast to the closely related tribes Robinieae and Sesbanieae.

1. Introduction

The tribe Loteae (Papilionoideae, Fabaceae), according to recent data, includes the tribe Coronilleae [1] and comprises 16 genera and about 275 species of legumes [2]. The tribe combines annual and perennial herbs, semishrubs and rarely shrubs naturally distributed in Eurasia, Africa, Australia and North and South America, with centers of species diversity in the Mediterranean region and California [3,4].
The molecular phylogeny of the tribe Loteae was reconstructed using the nrITS marker alone [1,5] or in combination with morphology [4]. Separate phylogenetic studies have been devoted to certain genera of the tribe: Ornithopus L. [6], Dorycnopsis Boiss. [7], Podolotus Benth. [8], Anthyllis L. [9,10], Coronilla L. [11] and Lotus L. [12,13,14,15]. These studies usually included individual representatives of other genera of the tribe Loteae but did not cover the entire tribe. The phylogenetic reconstructions were based either on nrITS alone [6,7,9,11] or on nrDNA and cpDNA regions [8,10,14,15]. At the current stage, the multi-species genera of the tribe seem monophyletic, and a close affinity of certain genera composing four main evolutionary lineages (i.e., Lotus (incl. Tripodion, Cytisopsis and Hammatolobium) + Acmispon (incl. Syrmatium and Ottleya) + Ornithopus + Hosakia, Anthyllis + Antopetitia, Coronilla + Podolotus, Hippocrepis + Scorpiurus) is not questioned, but the earliest radiation events and relationships between the lineages remain ambiguous. In addition, partial incongruence of tree topologies reconstructed separately by nuclear and plastid regions was demonstrated in the phylogeny of Anthyllis [10] and Lotus [14].
Many phylogenetic studies of various plant taxa were focused on incongruent tree topologies among different genomic compartments because these genes evolve independently and are influenced by biological processes [16]. The conflicts may also occur among plastid genes or trees constructed by different plastid sequences. The possible reasons for them may include heteroplasmy and heteroplasmic recombination; the transfer of genes among plastid, mitochondrial and nuclear genomes; positive selection; and differences in GC content [16]. Additionally, the slower evolution of plastid sequences compared to nuclear ones often leads to a lack of proper resolution in the relationship between individual taxa in phylogenies reconstructed by plastid markers, which can be overcome by analyzing complete sequences of plastids.
The number of land plant species with known complete plastid genomes is approaching 50,000. Plastomes are generally conservative in organization and usually comprise four compartments: a large single-copy region (LSC, large single-copy region), a small single-copy region (SSC, small single-copy region) and two inverted repeats separating them (IRs, inverted repeats). However, in several plant lineages, the plastomes exhibit significant variability.
Despite the growth in research on sequencing the whole plastid genomes in the legume family, the degree of study remains low. Only about 24% (184 out of 770) of genera and about 1.5% (319 out of 22,000) of legume species had complete plastid genomes published in GenBank by 2021 [17]. The legume family has undergone numerous rearrangements in the plastomes, such as inversions, expansion, contraction of the genome, loss and occasional regain of a typical inverted repeat, loss of genes and introns, and accumulation of repeats [18]. Some of these changes may mark a particular group, while others occur independently in different clades [18]. The largest number of such changes was noted in the subfamily Papilionoideae. Many of the changes are related specifically to inverted repeats (IRs).
The Loteae tribe belongs to the so-called “50-kb inversion clade”, whose members have an inversion of about 50 kb in the LSC of the plastome. Within this clade, Loteae belongs to the so-called NPAAA (non-protein amino acid accumulating) clade, which includes the most economically significant cultivated legume species [19]. Molecular phylogenetic studies on the plastid site trnK-matK clearly show that the tribe Loteae belongs to the Robinioid clade. The members of the Robinioid clade (i.e., the tribes Robinieae, Sesbanieae and Loteae) have been shown to possess both inverted repeats in their plastomes, in contrast to its sister group, the so-called IRLC (Inverted Repeat-Lacking Clade), whose members lack one of the IRs. The genus Sesbania Adans. distributed in the Paleo- and Neotropics appears sister to the tribe Loteae, while the tribe Robinieae, which includes several genera of woody, shrubby and sometimes herbaceous plants from the tropics and subtropics, is a sister group to “Loteae plus Sesbania” in many previous studies [19,20,21,22]. However, in more recent phyloplastomic analyses, Robinieae was more closely related to Loteae than Sesbanieae [17,18]. Both Robinia L. and Sesbania revealed the presence of structural rearrangements of the plastome. Sesbania drummondii (Rydb.) Cory, S. cannabina (Retz.) Poir. and S. grandiflora (L.) Poir. have a 50-kilobase reversion, which distinguishes them from all representatives of the “50-kb inversion clade” [18]. Robinia pseudoacacia L. possesses a 36 kb inversion in the LSC [23].
Until recently, plastid genomes in the Loteae tribe were known only for a small number of species: Lotus japonicus (Regel) K.Larsen [24], L. corniculatus L. [25], Coronilla varia L. [26], C. valentina L. ssp. glauca (L.) Batt. and Anthyllis barba-jovis L. [27]. It is noteworthy that these Loteae plastomes did not exhibit structural rearrangements. At the same time, for most genera of the tribe, there are no data on complete plastomes yet. This study aimed to obtain new information on the plastid genome structure of the Loteae representatives in order to assess plastid genome variability and reconstruct phylogenetic relationships within the tribe Loteae. With this purpose, we performed the following: 1. sequencing, assembly and annotation of 13 complete plastid genomes of representatives of large genera of the tribe Loteae (i.e., Acmispon, Hippocrepis and Lotus) and Robinia pseudoacacia using our own data; 2. assembly and annotation of three (Anthyllis vulneraria, Hippocrepis emerus, and Ornithopus perpusillus) plastomes using GenBank sequence read archive (SRA) data; 3. structural and phylogenetic analyses of the assembled plastomes.

2. Results

2.1. Comparative Analysis of the Loteae Plastomes

All sixteen newly assembled Loteae plastomes showed a quadripartite structure with an overall length ranging from 150,069 (Lotus tetragonolobus) to 152,206 (Acmispon glaber) base pairs (bp) (Table 1). The mean coverage depth of the plastomes was as follows: Acmispon americanus ~210×, A. glaber ~64×, A. parviflorus ~120×, Anthyllis vulneraria ~394×, Hippocrepis biflora ~87×, H. ciliata ~82×, H. emerus ~234×, Ornithopus perpusillus ~68×, Lotus graecus ~22×, L. palustris ~36×, Lotus dorycnium* ~485×, Lotus herbaceus ~33×, Lotus hirsutus ~39×, Lotus tetragonolobus* ~352×, Lotus conjugatus* ~1940×, Lotus ornithopodioides* ~823×, Robinia pseudoacacia ~660× (*—the mean coverage depth was assessed in Oxford nanopore reads). The LSC regions ranged from 81,319 bp (Hippocrepis biflora) to 83,583 bp (Acmispon glaber) in size, whereas the SSC ranged from 18,171 bp (Acmispon parviflorus) to 18,348 bp (Hippocrepis emerus); the pair of inverted repeats separated by the small single copy region ranged from 24,961 bp (Ornithopus perpusillus) to 25,317 bp (Hippocrepis ciliata).
The overall GC content varied slightly between 35.8% and 36.23%. The sixteen Loteae plastomes contained 127 genes, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes (Figure 1). The plastome of Robinia also possesses the quadripartite structure with all compartments being longer than those of the Loteae representatives (Table 1), and it does not contain the rps16 gene, like conspecific plastomes (accessions NC_026684 and MT120809).
All assembled plastomes showed relative stability of inverted repeat borders with no substantial shifts (Figure 2). Thus, LSC/IRa (JLA), SSC/IRa (JSA) and LSC/IRb (JLB) junctions were found in the rpl2-trnH spacer, in the ycf1 gene and in the rps19-rpl2 spacer (except for Lotus hirsutus plastome with JLB within rps19), respectively. In the plastomes of Anthyllis, all Hippocrepis species and two Acmispon species (A. parviflorus and A. americanus), the SSC/IRb junction (JSB) was placed between the ycf1 fragment and ndhF gene, while in the plastomes of Robinia, Ornithopus, all Lotus species and Acmispon glaber, the JSB crossed the 3` end of the ndhF gene.
All annotated genes in Loteae plastomes retained the same relative position, suggesting full collinearity (Supplementary Figure S1). A small number of perfect dispersed repeats (with a length exceeding 30 bp) was detected, with their relative length around 1% of the total plastome (Table 2).
The most variable sites of the studied plastomes were found in the petN-trnC and rps16-accD spacers from the LSC region and in the ycf1 gene within the SSC (Figure 3).

2.2. Phylogenetic Analysis

Bayesian inference resulted in the only tree (with posterior probability = 1), and, in the ML analysis, the same topology was reconstructed with all the clades attaining maximal support; therefore, only the Bayesian tree is presented (Figure 4). All genera represented by two or more species have formed genus-specific clades, namely the Hippocrepis clade, Coronilla clade, Anthyllis clade, Lotus clade and Acmispon clade. The genus Ornithopus, represented in this study by a single species, O. perpusillus, is in a sister position to the Acmispon clade. The Acmispon + Ornithopus clade is, in turn, sister to the Lotus clade. The Lotus clade is subdivided into the so-called Northern clade, which includes representatives of sections Lotus, Dorycnium and Bonjeanea, and the Southern clade, represented in this study by representatives of sections Lotea and Tetragonolobus. The Anthyllis clade is sister to the ((Acmispon + Ornithopus) + Lotus) clade, and Coronilla is sister to the (((Acmispon + Ornithopus) + Lotus) + Anthyllis) clade. The Hippocrepis clade is sister to the clade comprising all other studied genera. Thus, among the sampled specimens, the genus Hippocrepis is the most distant from other genera of Loteae according to the whole plastome sequence (Figure 4).

3. Discussion

For this study, we have assembled 14 complete plastid genomes using our own data, and another three plastomes have been assembled from GenBank SRA, sampling species from five genera of the tribe Loteae, namely Hippocrepis, Anthyllis, Lotus, Acmispon and Ornithopus, and Robinia pseudoacacia from the tribe Robinieae. With the inclusion of Coronilla complete plastome data from GeneBank, the number of Loteae genera studied increased to six out of sixteen accepted genera.
As a whole, the studied plastomes of the tribe Loteae turned out to be very conservative both in their general structure and the gene composition, and they all share the same order of the genes as many unrearranged “50-kb inversion clade” plastomes.
The sampled Loteae plastome length variation was also very moderate. As is known, large length variations in the plastomes of photosynthetic angiosperms may be associated either with the loss of inverted repeats or a significant expansion/contraction of inverted repeats (e.g., in Leguminosae [18,28], Geraniaceae [29,30], Apiaceae [31,32], etc.), and none of these events have been observed in the Loteae plastomes to date.
Major structural rearrangements have also not been found, unlike the Robinia and Sesbania genera from related tribes [18,22]. The newly assembled plastome of Robinia pseudoacacia showed complete collinearity with two conspecific plastomes that have lost the rps16 gene (GenBank accessions NC_026684 and MT120809) but differs from both in length, implying possible remarkable intraspecific plastome length heterogeneity in Robinia pseudoacacia. It is supposed that abundance in dispersed repeats facilitates plastomic rearrangements [33,34]. However, the direct causal effect is not obvious; the presence of dispersed repeats is rather a necessary but not sufficient condition for inversion occurrence, and the similar relative length of dispersed repeats in the Robinia and Loteae plastomes (Table 2) supports this point of view (see also discussion in [18]).
Comparative genomic analysis revealed several regions (petN-trnC and rps16-accD spacers from the LSC region, and in the ycf1 gene within the SSC) as the most variable and potentially useful for phylogenetic purposes. It has been shown earlier that variation in the ycf1 gene is associated with adaptations to high-altitude conditions (Saxifraga species [35]) or low-light conditions (the tribe Oenantheae of the Umbelliferae family [36]). However, among the studied representatives of the tribe Loteae, there are no high-altitude species or species from shady habitats. It is highly likely that some of the variability in this gene in the Loteae plastomes is associated with other factors.
Though our study covered only a few species from each of the multi-species genera, which contain from five (Ornithopus) to about one hundred twenty-five (Lotus) currently accepted species [2], the most probable tree inferred represents the relationships of the main evolutionary lineages of the Loteae tribe. Despite incomplete sampling of Loteae taxa in this study, we found several important correlations between the tree topology based on complete plastomes and those from previous studies, which were based on a limited number of plastid DNA markers [10] or a combination of ITS and plastid markers [8]. The first important topological similarity is the sister relationships between the clade (Lotus + Tripodion + Cytisopsis + Hammatolobium) and the primarily American clade (Acmispon (incl. Syrmatium and Ottleya) + Hosackia + Ornithopus + Dorycnopsis + Kebirita) [10]. A similar clustering pattern was found in the study by Degtjareva et al. [8] based on a combined dataset of ITS and two plastid markers. In the present study, the first clade includes only Lotus, and the second includes Acmispon and Ornithopus; however, their sister relationships are highly supported. Lotus species have split into two highly supported clades: the Northern clade (with a presumable ancestral area in Europe and North Asia) and the Southern clade (with the corresponding area in Macaronesia, Africa and S Asia). This subdivision is consistent with the results obtained previously from a more representative set of species based on two plastid markers only [14].
The second feature worth noting is the early divergence of Hippocrepis within Loteae. In the study by Degtjareva et al. [10], the clade (Hippocrepis + Scorpiurus) seemed to be the earliest diverged group of Loteae, following from the Bayesian inference analysis based on a set of three plastid markers, but the low supported position of the clade (Coronilla + Podolotus) left open the question of the basalmost branch. In the present study, the first diverged clade of Loteae is clearly represented by Hippocrepis, not Coronilla. The inclusion of the remaining genera of the Loteae, including monotypic genera, in future studies of complete plastid genomes will clarify the details and the order of divergence within the main phylogenetic lineages of the tribe Loteae.

4. Materials and Methods

4.1. Taxon Sampling and Sequencing

For the analysis of the whole plastid genome, we chose the following representatives of the tribe Loteae: Acmispon americanus (Nutt.) Rydb., A. glaber (Vogel) Brouillet ssp. glaber, A. parviflorus (Benth.) D.D.Sokoloff, Hippocrepis biflora Spreng., H. ciliata Willd., Lotus graecus L., L. palustris Willd., L. dorycnium L. ssp. lagunae, Lotus dorycnium ssp. herbaceus (Vill.) Kramina & D.D. Sokoloff, L. hirsutus L., L. tetragonolobus L., L. conjugatus L., and L. ornithopodioides L. The leaves of Acmispon americanus, A. glaber, A. parviflorus, Lotus palustris, L. graecus, L. dorycnium ssp. lagunae, Lotus dorycnium ssp. herbaceus, L. hirsutus, L. tetragonolobus, L. conjugatus and L. ornithopodioides, which were sampled for DNA isolation from living plants grown in the greenhouse of the Lomonosov Moscow State University (see Table 3 for the origin of seed material). The leaves of Hippocrepis ciliata and H. biflora were taken from silica-dried material collected in the wild (see Table 3 for voucher information).
The total genomic DNA was extracted from fresh (ca. 100 mg of leaf tissues) or silica-dried (ca. 20 mg of leaf tissue) leaves with NucleoSpin Plant II kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. Fragmentation of DNA was performed using an S220 focused-ultrasonicator (Covaris, Woburn, MA, USA), and DNA purification was performed using Agencourt AMPure XP beads (Beckman Coulter Co., Brea, CA, USA). Paired-end Illumina libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. The library was sequenced using an Illumina Nextseq500 instrument with a read length of 75 bp in paired-end mode.
The total genomic DNA from four species (Lotus tetragonolobus, Lotus conjugatus ssp. requienii, Lotus ornithopodioides and Lotus dorycnium ssp. lagunae) was additionally sequenced using Oxford nanopore technology. DNA Oxford nanopore libraries were prepared with Native Barcoding Kit 24 V14 (ONT, Oxford, UK) according to the manufacturer’s pcr-free protocol. The DNA library preparation consists of several steps: (1) DNA repair (FFPE) and end-prep for optimizing DNA quality; (2) preparing DNA sequence ends for barcode and adapter attachment, ligate Native barcodes supplied in the kit, and ligate sequencing adapters (3) preparing flow cell (R10.4.1) for sequencing (priming the flow cell). The DNA libraries were loaded into the R10.4.1 MinION Flowcell, and sequencing was performed using MinKnow software version 24.06.10 from ONT.

4.2. Chloroplast Genome Assembly and Annotation

The resulting Illumina reads were processed using Trimmomatic version 0.39 [37], and de novo assembly was performed using SPAdes toolkit version 4.0.0 [38]. Some scaffolds of the assembly of Acmispon parviflorus, Hippocrepis biflora, H. ciliata, Lotus graecus, and L. palustris contained stretches of undetermined bases (N), which were clarified by Sanger sequencing. Primers for amplification and sequencing are presented in Supplementary Table S1.
Oxford nanopore reads were processed with Canu assembler version 2.2 [39] and polished with Illumina reads using Polypolish tool version 0.6.0 [40].
Assembled scaffolds showing homology to plastid genomes were joined by overlapping ends.
In addition, the raw data of three representatives of the tribe Loteae Anthyllis vulneraria L., Hippocrepis emerus (L.) Lassen and Ornithopus perpusillus L. were retrieved from Sequence Read Archive in GenBank (accessions ERR5554795, ERR5529366 and ERR5529506, respectively), and the complete plastome sequences were assembled as described above (deposited in GenBank, accessions BK068666, BK068667 and BK068668, respectively).
To check the accuracy of assembly, trimmed paired reads were mapped to the whole assembled plastome followed by manual inspection in Tablet version 1.21.02.08 [41].
Plastome annotations were carried out with the web application GeSeq version 2.0.3 [42] and inspected using Artemis annotation tool version 16.0.0 [43]. Plastome gene maps were drawn using OGDraw version 1.3.1 [44], and IR border positions were visualized with IRscope version 0.1 tool [45]. Dispersed repeat content was explored using the repeat finder module in the Unipro UGENE package version 37.0 [46] with minimal length of perfect repeats restricted to 30 bases.

4.3. Comparative Analysis of the Loteae Plastomes

Plastome sequences were aligned using MAFFT version 7.471 [47] and inspected manually in Bioedit version 7.2.5 [48]. Regions where positional homology could not be firmly determined were excluded, along with the gap-rich positions and regions containing small inversions. The nucleotide divergence values (Pi) of plastid genomes were assessed in DnaSP program version 5.0 [49], with the window length and sliding step size set to 600 and 200 bp, respectively. Collinearity of the assembled plastomes of the representatives of Loteae together with two outgroups (Robinia pseudoacacia and Sesbania cannabina) was estimated using the Mauve program version 20150226 [50].

4.4. Phylogenetic Analysis

For phylogenetic analyses, seventeen newly assembled plastomes were combined with plastomes of Lotus japonicus (GenBank accession AP002983), L. corniculatus (MT528596), Coronilla varia (MW125582), C. valentina (ON009080), Anthyllis barba-jovis (ON009079) and Sesbania cannabina (Retz.) Poir. (NC_057145).
Phylogenetic analyses were performed for the whole genome alignment using Bayesian approach and maximum likelihood method. In all analyses, the plastomes of Robinia and Sesbania were specified as outgroups. The Bayesian phylogenetic reconstruction was performed via MrBayes v.3.2.6 [51] using four simultaneous runs of 20 million generations and four chains sampling every 1000th generation. The first million generations were discarded as burn-in, and effective sample size was evaluated using Tracer v.1.7.1 [52]. The effective sample sizes were > 200 for all statistics in all datasets, suggesting that the run length was adequate. The maximum likelihood (ML) phylogenetic reconstruction was performed by IQ-tree version 2.1.1 [53], and internal branch support was assessed with the ultrafast bootstrap approximation [54] using 10 thousand replications. To account for differences in variability and nucleotide composition across plastome compartments, LSC, SSC and inverted repeat sequences were treated as separate partitions with unlinked parameters of GTR + Г model according to the best scheme found in PartitionFinder version 2.1.1 [55].

5. Conclusions

The new data on 16 plastid genomes have expanded our knowledge of the characteristics of Loteae plastomes and demonstrated their structural conservation in contrast with the closely related tribes Robinieae and Sesbanieae. Phylogenetic analyses of all available Loteae plastome data resulted in highly supported and completely resolved relationships representing a backbone of plastid phylogeny.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/plants14040618/s1. Figure S1: Collinearity of the 16 assembled plastomes in Loteae, Robinia pseudoacacia and Sesbania cannabina; Table S1: Primers for amplification of unassembled regions of plastomes for Sanger sequencing.

Author Contributions

T.E.K. conceived the study; S.V.P. cultivated living plants in the greenhouse; Y.O.K.-G. collected samples in the wild; T.E.K. and Y.O.K.-G. extracted DNA for next-generation sequencing; T.E.K., Y.O.K.-G., A.A.K. and O.V.N. constructed DNA libraries; A.A.K. conducted next-generation sequencing of DNA libraries; T.H.S. assembled and annotated the plastid genomes and performed data analysis; T.E.K. and T.H.S. drafted the manuscript; T.H.S. reviewed the manuscript critically; T.E.K. carried out the project administration and funding acquisition. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Russian Science Foundation, project 23-24-00052.

Data Availability Statement

The plastome sequence data presented in this study are deposited in GenBank (accession numbers PQ539367-PQ539379, PQ636879, BK068666-BK068668). The raw data are deposited in GenBank within BioProject number PRJNA1206441, SRA accession numbers SRX27262107-SRX27262120.

Acknowledgments

We are very grateful to Maria Logacheva and Anna Speranskaya for their assistance in sequencing plastid genomes, to the staff of the botanical gardens and Zoya Akulova-Barlow for sending seed material, to Galina Degtjareva for providing Robinia pseudoacacia DNA material and to Dmitry Sokoloff for a useful discussion of the results.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Allan, G.J.; Porter, J.M. Tribal delimitation and phylogenetic relationships of Loteae and Coronilleae (Faboideae: Fabaceae) with special reference to Lotus: Evidence from nuclear ribosomal ITS sequences. Amer. J. Bot. 2000, 87, 1871–1881. [Google Scholar] [CrossRef]
  2. Legume Phylogeny Working Group (LPWG); Andrella, G.C.; Atahuachi Burgos, M.; Bagnatori Sartori, Â.L.; Balan, A.; Bandyopadhyay, S.; Barbosa Pinto, R.; Barrett, R.; Boatwright, J.S.; Borges, L.M.; et al. The World Checklist of Vascular Plants (WCVP): Fabaceae, 2023v.4; Govaerts, R., Ed.; Royal Botanic Gardens Kew: Kew, UK, 2023. [Google Scholar] [CrossRef]
  3. Sokoloff, D.D. On taxonomy and phylogeny of the tribe Loteae DC. (Leguminosae). Byull. Moskovsk. Obshch. Isp. Prir. Otd. Biol. 2003, 108, 35–48. (In Russian) [Google Scholar]
  4. Sokoloff, D.D.; Degtjareva, G.V.; Endress, P.K.; Remizowa, M.V.; Samigullin, T.H.; Valiejo-Roman, C.M. Inflorescence and early flower development in Loteae (Leguminosae) in a phylogenetic and taxonomic context. Int. J. Plant Sci. 2007, 168, 801–833. [Google Scholar] [CrossRef]
  5. Allan, G.J.; Zimmer, E.A.; Wagner, W.L.; Sokoloff, D.D. Molecular phylogenetic analyses of tribe Loteae (Leguminosae): Implications for classification and biogeography. In Advances in Legume Systematics; Klitgaard, B.B., Bruneau, A., Eds.; Royal Botanic Gardens: Kew, UK, 2003; Volume 10, pp. 371–393. [Google Scholar]
  6. Degtjareva, G.V.; Valiejo-Roman, C.M.; Kramina, T.E.; Mironov, E.M.; Samigullin, T.H.; Sokoloff, D.D. Taxonomic and phylogenetic relationships between Old World and New World members of the tribe Loteae (Leguminosae): New insights from molecular and morphological data, with special emphasis on Ornithopus. Wulfenia 2003, 10, 15–50. [Google Scholar]
  7. Degtjareva, G.; Valiejo-Roman, C.; Samigullin, T.; Sokoloff, D. On generic rank and phylogenetic relationships of Dorycnopsis Boiss. (Leguminosae, Loteae). An. Jardín Botánico Madr. 2006, 63, 41–50. [Google Scholar] [CrossRef]
  8. Degtjareva, G.V.; Samigullin, T.H.; Vallejo-Roman, C.M.; Sokoloff, D.D. Phylogenetic placement of Podolotus suggests independent origin of lomentaceous fruits in Coronilla and Hippocrepis (Leguminosae: Loteae). Pakistan J. Bot. 2010, 42, 11–25. [Google Scholar]
  9. Nanni, L.; Ferradini, N.; Taffetani, F.; Papa, R. Molecular phylogeny of Anthyllis spp. Plant Biol. 2004, 6, 454–464. [Google Scholar] [CrossRef]
  10. Degtjareva, G.V.; Valiejo-Roman, C.M.; Samigullin, T.H.; Guara-Requena, M.; Sokoloff, D.D. Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution. Mol. Phylogenet. Evol. 2012, 62, 693–707. [Google Scholar] [CrossRef]
  11. Cano, A.L.; Gómez, P.S.; Martínez, J.F.J. A New Species of Coronilla (Loteae, Fabaceae) from Southeastern Spain: Evidence from Morphological and Molecular Data. Folia Geobot. 2012, 47, 317–335. [Google Scholar] [CrossRef]
  12. Degtjareva, G.V.; Kramina, T.E.; Sokoloff, D.D.; Samigullin, T.H.; Valiejo-Roman, C.M.; Antonov, A.S. Phylogeny of the genus Lotus (Leguminosae, Loteae): Evidence from nrITS sequences and morphology. Can. J. Bot. 2006, 84, 813–830. [Google Scholar] [CrossRef]
  13. Degtjareva, G.V.; Kramina, T.E.; Sokoloff, D.D.; Samigullin, T.H.; Sandral, G.; Valiejo-Roman, C.M. New data on nrITS phylogeny of Lotus (Leguminosae, Loteae). Wulfenia 2008, 15, 35–49. [Google Scholar]
  14. Kramina, T.E.; Degtjareva, G.V.; Samigullin, T.H.; Valiejo-Roman, C.M.; Kirkbride, J.H., Jr.; Volis, S.; Deng, T.; Sokoloff, D.D. Phylogeny of Lotus (Leguminosae: Loteae): Partial incongruence between nrITS, nrETS and plastid markers and biogeographic implications. Taxon 2016, 65, 997–1018. [Google Scholar] [CrossRef]
  15. Jaén-Molina, R.; Marrero-Rodríguez, Á.; Caujapé-Castells, J.; Ojeda, D.I. Molecular phylogenetics of Lotus (Leguminosae) with emphasis in the tempo and patterns of colonization in the Macaronesian region. Mol. Phylogenet. Evol. 2021, 154, 106970. [Google Scholar] [CrossRef]
  16. Xiao, T.-W.; Xu, Y.; Jin, L.; Liu, T.-J.; Yan, H.-F.; Ge, X.-J. Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ 2020, 8, e10155. [Google Scholar] [CrossRef]
  17. Choi, I.-S.; Cardoso, D.; de Queiroz, L.P.; de Lima, H.C.; Lee, C.; Ruhlman, T.A.; Jansen, R.K.; Wojciechowski, M.F. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. Front. Plant Sci. 2022, 13, 823190. [Google Scholar] [CrossRef]
  18. Lee, C.; Choi, I.-S.; Cardoso, D.; de Lima, H.C.; de Queiroz, L.P.; Wojciechowski, M.F.; Jansen, R.K.; Ruhlman, T.A. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. Plant J. 2021, 107, 861–875. [Google Scholar] [CrossRef]
  19. Cardoso, D.; de Queiroz, L.P.; Pennigton, R.T.; de Lima, H.C.; Fonty, E.; Wojciechowski, M.F.; Lavin, M. Revisiting the phylogeny of papilionoid legumes: New insight from comprehensively sampled early-branching lineages. Am. J. Bot. 2012, 99, 1991–2013. [Google Scholar] [CrossRef] [PubMed]
  20. Cardoso, D.; Pennington, R.T.; de Queiroz, L.P.; Boatwright, J.S.; VanWyk, B.-E.; Wojciechowski, M.F.; Lavin, M. Reconstructing the deep-branching relationships of the papilionoid legumes. S. Arf. J. Bot. 2013, 89, 58–75. [Google Scholar] [CrossRef]
  21. Lavin, M.; Herendeen, P.S.; Wojciechowski, M.F. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Syst. Biol. 2005, 54, 530–549. [Google Scholar] [CrossRef]
  22. Farruggia, F.T.; Lavin, M.; Wojciechowski, M.F. Phylogenetic systematics and biogeography of the pantropical genus Sesbania (Leguminosae). Syst. Bot. 2018, 43, 414–429. [Google Scholar] [CrossRef]
  23. Schwarz, E.N.; Ruhlman, T.A.; Sabir, J.S.; Hajrah, N.H.; Alharbi, N.S.; Al-Malki, A.L.; Bailey, C.D.; Jansen, R.K. Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids. J. Syst. Evol. 2015, 53, 458–468. [Google Scholar] [CrossRef]
  24. Kato, T.; Kaneko, T.; Sato, S.; Nakamura, Y.; Tabata, S. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 2000, 7, 323–330. [Google Scholar] [CrossRef] [PubMed]
  25. Jiang, W.; Ma, L.; Yi, D.; Pang, Y. The complete chloroplast genome sequence of Lotus corniculatus L. Mitochondr. DNA Part B 2021, 6, 189–190. [Google Scholar] [CrossRef] [PubMed]
  26. Zhao, Y.; Xi, Q.; Wei, X.; Fu, J.; Wang, Q.; He, H.; Ling, C.; Chang, T.; Zhao, Y. The complete chloroplast genome of Securigera varia (L.) Lassen. Mitochondr. DNA Part B 2021, 6, 900–901. [Google Scholar] [CrossRef] [PubMed]
  27. Wang, Z.-X.; Wang, D.-J.; Yi, T.-S. Does IR-loss promote plastome structural variation and sequence evolution? Front. Plant Sci. 2022, 13, 888049. [Google Scholar] [CrossRef] [PubMed]
  28. Kolodner, R.; Tewari, K.K. Inverted repeats in chloroplast DNA from higher plants. Proc. Natl. Acad. Sci. USA 1979, 76, 41–45. [Google Scholar] [CrossRef]
  29. Guisinger, M.M.; Kuehl, J.V.; Boore, J.L.; Jansen, R.K. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Mol. Biol. Evol. 2011, 28, 583–600. [Google Scholar] [CrossRef]
  30. Ruhlman, T.A.; Zhang, J.; Blazier, J.C.; Sabir, J.S.M.; Jansen, R.K. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. Am. J. Bot. 2017, 104, 559–572. [Google Scholar] [CrossRef]
  31. Plunkett, G.M.; Downie, S.R. Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae. Syst. Bot. 2000, 25, 648–667. [Google Scholar] [CrossRef]
  32. Samigullin, T.; Logacheva, M.; Terentieva, E.; Degtjareva, G.; Pimenov, M.; Valiejo-Roman, C. Plastid phylogenomic analysis of Tordylieae tribe (Apiaceae, Apioideae). Plants 2022, 11, 709. [Google Scholar] [CrossRef]
  33. Haberle, R.C.; Fourcade, H.M.; Boore, J.L.; Jansen, R.K. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J. Mol. Evol. 2008, 66, 350–361. [Google Scholar] [CrossRef]
  34. Lee, H.L.; Jansen, R.K.; Chumley, T.W.; Kim, K.J. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol. Biol. Evol. 2007, 24, 1161–1180. [Google Scholar] [CrossRef] [PubMed]
  35. Chen, Z.; Yu, X.; Yang, Y.; Wei, P.; Zhang, W.; Li, X.; Liu, C.; Zhao, S.; Li, X.; Liu, X. Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment. Genes 2022, 13, 1673. [Google Scholar] [CrossRef] [PubMed]
  36. Wen, J.; Zhu, J.W.; Ma, X.D.; Li, H.-M.; Wu, B.-C.; Zhou, W.; Yang, J.-X.; Song, C.-F. Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes. BMC Plant Biol. 2024, 24, 1140. [Google Scholar] [CrossRef]
  37. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef]
  38. Prjibelski, A.; Antipov, D.; Meleshko, D.; Lapidus, A.; Korobeynikov, A. Using SPAdes De Novo Assembler. Curr. Protoc. Bioinform. 2020, 1, e102. [Google Scholar] [CrossRef]
  39. Koren, S.; Walenz, B.P.; Berlin, K.; Miller, J.R.; Phillippy, A.M. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017, 27, 722–736. [Google Scholar] [CrossRef]
  40. Bouras, G.; Judd, L.M.; Edwards, R.A.; Vreugde, S.; Stinear, T.P.; Wick, R.R. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Microb. Genom. 2024, 10, 001254. [Google Scholar] [CrossRef]
  41. Milne, I.; Bayer, M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D. Tablet—Next generation sequence assembly visualization. Bioinformatics 2010, 26, 401–402. [Google Scholar] [CrossRef]
  42. Tillich, M.; Lehwark, P.; Pellizzer, T.; Ulbricht-Jones, E.S.; Fischer, A.; Bock, R.; Greiner, S. GeSeq—Versatile and Accurate Annotation of Organelle Genomes. Nucleic Acids Res. 2017, 45, W6–W11. [Google Scholar] [CrossRef]
  43. Carver, T.; Berriman, M.; Tivey, A.; Patel, C.; Böhme, U.; Barrell, B.G.; Parkhill, J.; Rajandream, M.-A. Artemis and ACT: Viewing, Annotating and Comparing Sequences Stored in a Relational Database. Bioinformatics 2008, 24, 2672–2676. [Google Scholar] [CrossRef] [PubMed]
  44. Greiner, S.; Lehwark, P.; Bock, R. OrganellarGenomeDRAW (OGDRAW) Version 1.3.1: Expanded Toolkit for the Graphical Visualization of Organellar Genomes. Nucleic Acids Res. 2019, 47, W59–W64. [Google Scholar] [CrossRef]
  45. Amiryousefi, A.; Hyvönen, J.; Poczai, P. IRscope: An online program to visualize the junction sites of chloroplast genomes. Bioinformatics 2018, 34, 3030–3031. [Google Scholar] [CrossRef]
  46. Okonechnikov, K.; Golosova, O.; Fursov, M.; UGENE Team. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics 2012, 28, 1166–1167. [Google Scholar] [CrossRef]
  47. Katoh, K.; Standley, D.M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
  48. Hall, T.A. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41, 95–98. [Google Scholar]
  49. Librado, P.; Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25, 1451–1452. [Google Scholar] [CrossRef]
  50. Darling, A.C.E.; Mau, B.; Blattner, F.R.; Perna, N.T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14, 1394–1403. [Google Scholar] [CrossRef]
  51. Ronquist, F.; Teslenko, M.; Van Der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck, J.P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61, 539–542. [Google Scholar] [CrossRef]
  52. Rambaut, A.; Drummond, A.J.; Xie, D.; Baele, G.; Suchard, M.A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 2018, 67, 901–904. [Google Scholar] [CrossRef]
  53. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; Von Haeseler, A.; Lanfear, R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [PubMed]
  54. Hoang, D.T.; Chernomor, O.; Von Haeseler, A.; Minh, B.Q.; Vinh, L.S. UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 2018, 35, 518–522. [Google Scholar] [CrossRef] [PubMed]
  55. Lanfear, R.; Frandsen, P.B.; Wright, A.M.; Senfeld, T.; Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 2016, 34, 772–773. [Google Scholar] [CrossRef] [PubMed]
Plants 14 00618 g001
Figure 1. A circular genome map of the Loteae plastid genomes. Genes within the circle are transcribed clockwise, while those outside the circle are transcribed counterclockwise. Genes belonging to different functional groups are shown with various colors. Intron containing genes are marked with asterisks.
Figure 1. A circular genome map of the Loteae plastid genomes. Genes within the circle are transcribed clockwise, while those outside the circle are transcribed counterclockwise. Genes belonging to different functional groups are shown with various colors. Intron containing genes are marked with asterisks.
Plants 14 00618 g001
Plants 14 00618 g002
Figure 2. IR-SC junction positions in plastomes of 16 species of Loteae and Robinia pseudoacacia.
Figure 2. IR-SC junction positions in plastomes of 16 species of Loteae and Robinia pseudoacacia.
Plants 14 00618 g002
Plants 14 00618 g003
Figure 3. Sliding window analysis of nucleotide diversity (Pi) along the whole plastome for the 16 aligned plastomes of Loteae.
Figure 3. Sliding window analysis of nucleotide diversity (Pi) along the whole plastome for the 16 aligned plastomes of Loteae.
Plants 14 00618 g003
Plants 14 00618 g004
Figure 4. The most probable phylogenetic tree (posterior probability PP = 1.0) reconstructed in Bayesian analysis of 23 complete plastome sequences. All internal branches gained highest support (PP = 1, UFB = 100%); scale bar corresponds to 0.01 substitution per site.
Figure 4. The most probable phylogenetic tree (posterior probability PP = 1.0) reconstructed in Bayesian analysis of 23 complete plastome sequences. All internal branches gained highest support (PP = 1, UFB = 100%); scale bar corresponds to 0.01 substitution per site.
Plants 14 00618 g004
Table 1. Summary of 16 complete plastomes of Loteae and Robinia pseudoacacia.
Table 1. Summary of 16 complete plastomes of Loteae and Robinia pseudoacacia.
TaxonTotal cpDNA Size (bp)Length of LSC Region (bp)Length of IR Region (bp)Length of SSC Region (bp)Total GC Content (%)
Acmispon americanus151,67983,07825,21418,17335.80
Acmispon parviflorus151,77183,17425,21318,17135.80
Acmispon glaber ssp. glaber152,20683,58325,21318,19735.80
Ornithopus perpusillus151,11383,01424,96118,17736.02
Lotus graecus151,11882,63425,12218,24036.04
Lotus palustris151,52483,01125,16018,19335.95
Lotus dorycnium ssp. lagunae150,68582,20125,11718,25036.02
Lotus dorycnium ssp. herbaceus151,07182,55825,13218,24936.01
Lotus hirsutus151,14482,57325,14718,27736.00
Lotus tetragonolobus150,06981,49825,12918,31336.21
Lotus conjugatus ssp. requienii151,09782,62825,13918,19136.11
Lotus ornithopodioides151,20182,65025,14518,26136.04
Anthyllis vulneraria151,86883,47325,08318,22935.94
Hippocrepis biflora150,23781,31925,31418,29036.23
Hippocrepis ciliata150,86281,90825,31718,32036.18
Hippocrepis emerus151,13082,17025,30618,34836.04
Robinia pseudoacacia155,30185,37025,66818,59535.90
Table 2. Statistics of perfect dispersed repeats (30 bp and longer) in the plastomes of 16 species of Loteae and Robinia pseudoacacia.
Table 2. Statistics of perfect dispersed repeats (30 bp and longer) in the plastomes of 16 species of Loteae and Robinia pseudoacacia.
Dispersed Repeats NumberDirect/Inverted Repeat Length, bpRelative Length, % of Plastome Length
DirectInverted
Acmispon americanus41629/390.88
Acmispon glaber ssp. glaber62706/771.02
Acmispon parviflorus54675/1401.08
Anthyllis vulneraria53622/1110.96
Hippocrepis biflora62744/791.08
Hippocrepis ciliata53698/1091.06
Hippocrepis emerus53721/1111.10
Ornithopus perpusillus72737/771.06
Lotus conjugatus ssp. requienii52652/770.96
Lotus dorycnium ssp. lagunae52654/770.96
Lotus graecus52654/770.96
Lotus dorycnium ssp. herbaceus63684/1071.04
Lotus hirsutus53678/1071.04
Lotus ornithopodioides53678/1071.04
Lotus palustris53654/1071.00
Lotus tetragonolobus62688/771.02
Robinia pseudoacacia50714/01.00
Table 3. Studied taxa, material origin, voucher information and GenBank accession numbers.
Table 3. Studied taxa, material origin, voucher information and GenBank accession numbers.
Taxon NameSeed or Herbarium Collection LocalityCoordinatesHerbarium VoucherGenBank Accession Number
Acmispon americanus (Nutt.) Rydb.Cult. in the greenhouse of the MSU, Moscow. Origin: USA, El Cerrito, California, Z. Akulova-Barlow37.904 N, 122.303 WMWPQ539379
Acmispon glaber (Vogel) Brouillet ssp. glaberCult. in the greenhouse of the MSU, Moscow. Origin: USA, Near Briones Reservoir, Contra Costa County, California, Z.Akulova-Barlow37.918 N, 122.203 WMWPQ539367
Acmispon parviflorus (Benth.) D.D.SokoloffCult. in the greenhouse of the MSU, Moscow. Origin: USA, Near Albion, Mendocino County, California, Z.Akulova-Barlow39.205 N, 123.701 WMWPQ539368
Hippocrepis biflora Spreng.Crimea: Sapun-gora hill, Sevastopol, Yu. Kopylov-Guskov, 202344.559 N, 33.544 EMWPQ539370
Hippocrepis ciliata Willd.Crimea: southern outskirts of Balaklava town, Yu. Kopylov-Guskov, 202344.492 N, 33.608 EMWPQ539371
Lotus graecus L.Cult. in the greenhouse of the MSU, Moscow. Origin: Crimea: Vinogradnoye, mount Castell, T. Kramina & S. Polevova, 202044.642 N, 34.384 EMWPQ539373
Lotus dorycnium ssp. herbaceus (Vill.) Kramina & D.D. SokoloffCult. in the greenhouse of the MSU, Moscow. Origin: Crimea: Ayu-Dag, T. Kramina & S. Polevova, 202044.566 N,
34.323 E		MWPQ539374
L. dorycnium L. ssp. lagunae (Ceresuela & Sanchis) P. P. Ferrer & RossellуCult. in the greenhouse of the MSU, Moscow. Origin: Spain, Alicante, Finestrat38.565 N,
0.212 W		MWPQ539369
Lotus hirsutus L.Cult. in the greenhouse of the MSU, Moscow. Origin: Spain, Valencia,
The Botanical Garden of the University
of Valencia. 2019. ES-0-VAL-476-97		–MWPQ539375
Lotus palustris Willd.Cult. in the greenhouse of the MSU, Moscow. Origin: Mediterranean Region. Cultivated in Argentina, A.M.Arambarri–MWPQ539377
L. tetragonolobus L.Cult. in the greenhouse of the MSU, Moscow. Origin: Mainz Bot. Garden, 388, 143-2020–MWPQ539378
L. conjugatus L. ssp. requienii (Mauri ex Sanguin.) GreuterCult. in the greenhouse of the MSU, Moscow. Origin: Mainz Bot. Garden, 386, 143-2020–MWPQ539372
L. ornithopodioides L.Cult. in the greenhouse of the MSU, Moscow. Origin: Mainz Bot. Garden, 387, 143-2020–MWPQ539376
Robinia pseudoacacia L.Cult. in the MSU, Moscow, Russia. Origin: Eastern N. America. Collected in 2006–MWPQ636879
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Samigullin, T.H.; Kopylov-Guskov, Y.O.; Nikitina, O.V.; Krinitsina, A.A.; Polevova, S.V.; Kramina, T.E. Sixteen New Complete Plastid Genomes in the Tribe Loteae (Leguminosae): Structure and Phylogenetic Analysis. Plants 2025, 14, 618. https://doi.org/10.3390/plants14040618

AMA Style

Samigullin TH, Kopylov-Guskov YO, Nikitina OV, Krinitsina AA, Polevova SV, Kramina TE. Sixteen New Complete Plastid Genomes in the Tribe Loteae (Leguminosae): Structure and Phylogenetic Analysis. Plants. 2025; 14(4):618. https://doi.org/10.3390/plants14040618

Chicago/Turabian Style

Samigullin, Tahir H., Yury O. Kopylov-Guskov, Olga V. Nikitina, Anastasiya A. Krinitsina, Svetlana V. Polevova, and Tatiana E. Kramina. 2025. "Sixteen New Complete Plastid Genomes in the Tribe Loteae (Leguminosae): Structure and Phylogenetic Analysis" Plants 14, no. 4: 618. https://doi.org/10.3390/plants14040618

APA Style

Samigullin, T. H., Kopylov-Guskov, Y. O., Nikitina, O. V., Krinitsina, A. A., Polevova, S. V., & Kramina, T. E. (2025). Sixteen New Complete Plastid Genomes in the Tribe Loteae (Leguminosae): Structure and Phylogenetic Analysis. Plants, 14(4), 618. https://doi.org/10.3390/plants14040618

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop