Genotypic characterization of Lactic acid bacteria in gut microbiome of freshwater fish

The present study focused on identification and genotypic characterization of Lactic acid bacteria (LAB) in the intestine of freshwater fish. 76 strains of LAB were isolated and identified by 16S rRNA gene sequences and hsp60 gene sequences as different strains of Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus fermentum, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus brevis, Lactobacillus reuteri, Lactobacillus salivarius, Pediococcus pentosaceus, Pediococcus acidilactici, Weissella paramesenteroides, Weissella cibaria, Enterococcus faecium, and Enterococcus durans. The hsp60 gene showed a higher level of sequence variation among the isolates examined, with lower interspecies sequence similarity providing more resolutions at the species level than the 16S rRNA gene. Phylogenetic tree derived from hsp60 gene sequences with higher bootstrap values at the nodal branches was more consistent as compared to phylogenetic tree constructed from 16S rRNA gene sequences. Closely related species L. plantarum and L. pentosus as well as species L. delbrueckii subsp. bulgaricus and L. fermentum were segregated in different cluster in hsp60 phylogenetic tree whereas such a distribution was not apparent in 16S rRNA phylogenetic tree. In silico restriction analysis revealed a high level of polymorphism within hsp60 gene sequences. Restriction pattern with enzymes AgsI and MseI in hsp60 gene sequences allowed differentiation of all the species including closely related species L. plantarum and L. pentosus, E. faecium and E. durans. In general, hsp60 gene with higher evolutionary divergence proved to be a better phylogenetic marker for the group LAB.     

Comprehensive dataset of mangrove tree weights in Southeast Asia

We assembled a dataset tabulating the weights of Thai and Indonesian mangrove trees that we measured between 1982 and 2001. We selected four Thai study sites in Phang Nga, Ranong, Satun, and Trat Provinces and one site in eastern Indonesia on Halmahera Island in Maluku Province. The stands in Ranong Province and on Halmahera Island were in primary forests with data collected in the 1980s and the remaining stands were in secondary forests with data collected later. We collected 124 tree samples from ten species (Avicennia alba, Bruguiera cylindrica, B. gymnorrhiza, Ceriops tagal, Rhizophora apiculata, R. mucronata, Sonneratia alba, S. caseolaris, Xylocarpus granatum, and X. moluccensis) and measured the root weights of 32 individuals of nine species (A. alba, B. cylindrica, B. gymnorrhiza, C. tagal, R. apiculata, R. mucronata, S. alba, S. caseolaris, and X. granatum). All sampled trees were subjected to a standardized protocol to obtain aboveground weights. The trunks were divided into horizontal segments from which the leaves and branches were collected separately. Roots were collected by winching them out of the ground, by trench digging, or by complete excavation. Thus, we were able to compile the weights of the trunk, branches, leaves, and roots of each tree sampled. Aerial roots were included in root weight measurements, although they were collected above ground. We compiled separate lists of trunk diameters, trunk heights, heights of the lowest living branches, and the heights of aerial roots on the trunks of trees in different size categories. Our dataset includes a wide range of tree sizes (maximum trunk diameter 48.9 cm), geographical locations (1°10′N–12°24′N, 98°32′E–123°49′E) and organ weights (trunks, branches, leaves, and roots), and therefore should prove useful in future biomass studies of mangrove forests.     

Diversity and abundance of coccinellids (Coleoptera: Coccinellidae) on trees in parks and tree rows of Belgrade

Harmonia axyridis is an invasive coccinellid species that was first recorded in Serbia in 2008. In order to establish whether after its arrival it became the dominant coccinellid species, we investigated the diversity and abundance of coccinelids on trees in parks and tree rows of Belgrade during 2015 and 2016. Thirteen coccinellid species were recorded in these investigations. Frequently occurring among them were Adalia bipunctata, A. decempunctata, Coccinella septempunctata, Exochomus quadripustulatus, Harmonia axyridis, H. quadripunctata, Oenopia conglobata, and Popylea quatuordecimpunctata. All of them had different dynamics of appearance during the vegetation. As a result of this, the values of their dominance in the coccinellid community constantly changed. However, only in the cases of H. axyridis, O. conglobata, and C. septempunctata were those values high enough for us to be able to say that they were dominant in terms of abundance during a certain period. Although the amounts of summer precipitation in Serbia were very different during 2015 and 2016, the trends of changes in the diversity of coccinellids throughout the growing season in these two years were similar.     

Reduced ant defenses in <Emphasis Type="Italic">Macaranga</Emphasis> myrmecophytes (Euphorbiaceae) infested with a winged phasmid <Emphasis Type="Italic">Orthomeria cuprinus</Emphasis>

Macaranga is a tree genus that includes many species of myrmecophytes, which are plants that harbor ant colonies within hollow structures known as domatia. The symbiotic ants (plant–ants) protect their host plants against herbivores; this defense mechanism is called ‘ant defense’. A Bornean phasmid species Orthomeria cuprinus feeds on two myrmecophytic Macaranga species, Macaranga beccariana and Macaranga hypoleuca, which are obligately associated with Crematogaster ant species. The phasmids elude the ant defense using specialized behavior. However, the mechanisms used by the phasmid to overcome ant defenses have been insufficiently elucidated. We hypothesized that O. cuprinus only feeds on individual plants with weakened ant defenses. To test the hypothesis, we compared the ant defense intensity in phasmid-infested and non-infested M. beccariana trees. The number of plant–ants on the plant surface, the ratio of plant–ant biomass to tree biomass, and the aggressiveness of plant–ants towards experimentally introduced herbivores were significantly lower on the phasmid-infested trees than on the non-infested trees. The phasmid nymphs experimentally introduced into non-infested trees, compared with those experimentally introduced into phasmid-infested trees, were more active on the plant surface, avoiding the plant–ants. These results support the hypothesis and suggest that ant defenses on non-infested trees effectively prevent the phasmids from remaining on the plants. Thus, we suggest that O. cuprinus feeds only on the individual M. beccariana trees having decreased ant defenses, although the factors that reduce the intensity of the ant defenses remain unclear.     

Phylogenetic analysis reveals the origins of tetraploid and hexaploid species in the Japanese <Emphasis Type="Italic">Lepisorus thunbergianus</Emphasis> (Polypodiaceae) complex

The Japanese Lepisorus thunbergianus complex contains diploid and tetraploid races of L. thunbergianus and a hexaploid species, L. mikawanus. Here, we performed molecular phylogenetic analysis on this complex to delimit species and to elucidate the evolutionary origins of tetraploid and hexaploid species. Chloroplast DNA (cpDNA) phylogeny supported the monophyly of the complex. Based on a single-copy nuclear gene (PgiC) tree, the tetraploid L. thunbergianus samples could be classified into two variants: an allotetraploid of hybrid origin between diploid L. thunbergianus and Japanese L. angustus and another allotetraploid of hybrid origin between diploid L. thunbergianus and an unknown diploid race of L. tosaensis. These variants can be recognized morphologically and distinguished from their parent species. Hence, here we described these allopolyploids as new species, L. nigripes and L. kuratae, respectively. The hexaploid species L. mikawanus has three types of PgiC alleles, each of which was derived from diploid L. thunbergianus, L. tosaensis, and Japanese L. angustus, while cpDNA shows that it is included in Japanese L. thunbergianus clade. Based on the cpDNA phylogeny and PgiC nucleotide sequences, we therefore concluded that L. mikawanus is an allohexaploid that originated through hybridization between tetraploid species, L. nigripes and an unknown ancestral diploid race of L. tosaensis.     

Phylogenetic analyses of <Emphasis Type="Italic">Symbiodinium</Emphasis> isolated from <Emphasis Type="Italic">Waminoa</Emphasis> and their anthozoan hosts in the Ryukyu Archipelago,southern Japan

It is known that the genus Waminoa (order Acoela, Family Convolutidae) associates with anthozoans (Scleractinia, Octocorallia, Zoantharia) and feeds on the mucus of their host. Despite the close relationship between Waminoa and its host species, it is known from phylogenetic analyses of sequences of the internal transcribed spacer 2 of ribosomal DNA (ITS-2) that photosymbiotic Symbiodinium isolated from Waminoa are different from the Symbiodinium of their anthozoan hosts. Additionally, Waminoa inherit their Symbiodinium and Amphidinium via vertical transmission. In the current study, we looked for and collected Waminoa from different anthozoan hosts from the Ryukyu Archipelago in southern Japan, and then examined the Symbiodinium of Waminoa as well as hosts’ Symbiodinium, and utilized sequences of the hyper-variable non-coding region of the plastid minicircle (psbA^ncr) in order to re-examine the diversity of Symbiodinium within Waminoa. In the resulting psbA^ncr phylogenetic tree, all Symbiodinium within Waminoa comprised a unique group within Clade C, all with the same genotype in the psbA^ncr phylogenetic tree. Our results reconfirm that most Waminoa host their own lineage of Symbiodinium, and demonstrate that Waminoa are also found on azooxanthellate anthozoan hosts, as we found Waminoa on Siphonogorgia sp., expanding their potential known habitat. Additionally, two Symbiodinium from Waminoa from both shallow (4 m) and mesophotic (32 m) depths were not included in main group of Symbiodinium from Waminoa in the ITS-2 phylogenetic tree, although we could not acquire psbA^ncr sequences for these specimens. Therefore it is possible that undetected Symbiodinium diversity may yet exist within Waminoa, and future work at shallow to mesophotic depths examining both zooxanthellate and azooxanthellate hosts may find more Waminoa and Symbiodinium diversity.     

Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes

GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress responses, and functional divergences. In our study, 597 GELP genes were identified from six Rosaceae genomes (i.e., Fragaria vesca, Prunus persica, Prunus avium, Prunus mume, Pyrus bretschneideri, and Malus domestica) by a comprehensive analysis. All GELP genes were further divided into ten subfamilies based on phylogenetic tree analysis. Subfamily D and subfamily E are the two largest subfamilies. Microcollinearity analysis suggested that WGD/segmental events contribute to the expansion of the GELP gene family in M. domestica and P. bretschneideri compared to F. vesca, P. persica, P. avium, and P. mume. Some PbGELPs were expressed during the fruit development of P. bretschneideri and pollen tubes, indicating their activity in these tissues. The expression divergence of PbGELP duplication gene pairs suggests that many mutations were allowed during evolution, although the structure of GELP genes was highly conserved. The current study results provided the feasibility to understand the expansion and evolution patterns of GELP in Rosaceae genomes, and highlight the function during P. bretschneideri fruits and pollen tubes development.     

Communities of arbuscular mycorrhizal fungi under <Emphasis Type="Italic">Picconia azorica</Emphasis> in native forests of Azores

Arbuscular mycorrhizal fungi (AMF) from the rhizosphere of the endemic Laurisilva tree, Picconia azorica, were characterised at two sites in each of two Azorean islands (Terceira and São Miguel). Forty-six spore morphotypes were found, and DNA extraction was attempted from individual spores of each of these. DNA was obtained from 18 of the morphotypes, from which a 1.5 kb long fragment of the nuclear ribosomal RNA gene (SSU-ITS-LSU) was sequenced. A total of 125 AMF sequences were obtained and assigned to 18 phylotypes. Phylogenetic analysis revealed sequences belonging to the families, Acaulosporaceae, Archaeosporaceae, Claroideoglomeraceae, Gigasporaceae and Glomeraceae. Phylotype richness changed between islands and between sampling sites at both islands suggesting that geographical and historical factors are determinant in shaping AMF communities in native forest of Azores. Ecological analysis of the molecular data revealed differences in AMF community composition between islands. In Terceira, the rhizosphere of P. azorica was dominated by species belonging to Acaulosporaceae and Glomeraceae, while São Miguel was dominated by members of Glomeraceae and Gigasporaceae. This is the first molecular study of AMF associated with P. azorica in native forest of the Azores. These symbiont fungi are key components of the ecosystem. Further research is needed to develop their use as promoters of plant establishment in conservation and restoration of such sites.     

Diversity of <Emphasis Type="Italic">A</Emphasis> mating type in <Emphasis Type="Italic">Lentinula edodes</Emphasis> and mating type preference in the cultivated strains

Diversity of A mating type in Lentinula edodes has been assessed by analysis of A mating loci in 127 strains collected from East Asia. It was discovered that hypervariable sequence region with an approximate length of 1 kb in the A mating locus, spanning 5′ region of HD2-intergenic region-5′ region of HD1, could represent individual A mating type as evidenced by comprehensive mating analysis. The sequence analysis revealed 27 A mating type alleles from 96 cultivated strains and 48 alleles from 31 wild strains. Twelve of them commonly appeared, leaving 63 unique A mating type alleles. It was also revealed that only A few A mating type alleles such as A1, A4, A5, and A7 were prevalent in the cultivated strains, accounting for 62.5% of all A mating types. This implies preferred selection of certain A mating types in the process of strain development and suggests potential role of A mating genes in the expression of genes governing mushroom quality. Dominant expression of an A mating gene HD1 was observed from A1 mating locus, the most prevalent A allele, in A1-containing dikaryons. However, connections between HD1 expression and A1 preference in the cultivated strains remain to be verified. The A mating type was highly diverse in the wild strains. Thirty-six unique A alleles were discovered from relatively small and confined area of mountainous region in Korean peninsula. The number will further increase because no A allele has been recurrently observed in the wild strains and thus newly discovered strain will have good chances to contain new A allele. The high diversity in small area also suggests that the A mating locus has evolved rapidly and thus its diversity will further increase.     

Nucleotide polymorphisms of candidate genes of adaptive significance in the ural populations of <Emphasis Type="Italic">Larix sibirica</Emphasis> Ledeb.

The objectives of conservation and sustainable forest management require in depth study of genomes of woody plants and definition of their intraspecific genetic diversity. In recent years, an approach was developed based on the study of “candidate genes” that can potentially be involved in the formation of adaptive traits. In this study, we investigated nucleotide polymorphism of several adaptive candidate genes in the populations of Siberian larch (Larix sibirica Ledeb.) in the Urals. Representatives of this genus are among the most valuable and widely distributed forest tree species in Russia. From ten selected gene loci in the genome of L. sibirica, we isolated and investigated three loci, one of which (ABA-WDS) was sequenced in L. sibirica for the first time. The total length of the analyzed sequence in each individual amounted to 2865 bp. The length of locus alignment was from 360 bp to 1395 bp. In total, we identified 200 polymorphic positions. The most conservative is locus 4CL1-363, and the most polymorphic is locus sSPcDFD040B03103-274. The studied populations of L. sibirica are characterized by a high level of nucleotide polymorphism in comparison with other species and genuses (Picea, Pinus, Pseudotsuga, Abies) conifers plants (Hd = 0.896; π = 0.007; θ_W = 0.015). The most selectively neutral polymorphism (D _T =–0.997) was attributed to locus 4CL1-363, and polymorphism with high probability of adaptability (D _T =–1.807) was determined for the ABA-WDS locus. We identified 54 SNP markers, only five of which were nonsynonymous (9.26%) replacements. The average frequency of SNPs in the three studied loci of L. sibirica was one SNP in 53 bp. We detected unique SNP markers for eight populations, which could potentially be used to identify populations. Populations that are characterized by the highest number of unique SNP markers can be recommended for selection in order to preserve the gene pool of the species.     

QTL mapping of mandarin (<Emphasis Type="Italic">Citrus reticulata</Emphasis>) fruit characters using high-throughput SNP markers

Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F₁ population derived from ‘Fortune’ × ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (Citrus clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. A cluster of QTLs for flavedo color space values L, a, b, and a/b and juice color space values a and a/b were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.     

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, <Emphasis Type="Italic">Tuber arnoldianum</Emphasis> sp. nov.

During a study comparing the ectomycorrhizal root communities in a native forest with those at the Arnold Arboretum in Massachusetts (USA), the European species Tuber borchii was detected on the roots of a native red oak in the arboretum over two successive years. Since T. borchii is an economically important edible truffle native to Europe, we conducted a search of other roots in the arboretum to determine the extent of colonization. We also wanted to determine whether other non-native Tuber species had been inadvertently introduced into this 140-year-old Arboretum because many trees were imported into the site with intact soil and roots prior to the 1921 USDA ban on these horticultural practices in the USA. While T. borchii was not found on other trees, seven other native and exotic Tuber species were detected. Among the North American Tuber species detected from ectomycorrhizae, we also collected ascomata of a previously unknown species described here as Tuber arnoldianum. This new species was found colonizing both native and non-native tree roots. Other ectomycorrhizal taxa that were detected included basidiomycetes in the genera Amanita, Russula, Tomentella, and ascomycetes belonging to Pachyphlodes, Helvella, Genea, and Trichophaea. We clarify the phylogenetic relationships of each of the Tuber species detected in this study, and we discuss their distribution on both native and non-native host trees.     

Molecular taxonomy of five species of microfungi on <Emphasis Type="Italic">Alnus</Emphasis> spp. from Italy

Five new fungal taxa found on Alnus, a valuable timber tree widely distributed in Europe, are described using morphology and multigene phylogenetic analyses. The new Dothideomycetes, Helminthosporium italicum, Dothiorella guttulata, and Prosthemium alni, and Sordariomycetes, Ditopella aseptatospora and Cryptosporella alni-cordatae, are compared with similar taxa and the differences are discussed.     

Post-release evaluation of non-target effects of <Emphasis Type="Italic">Torymus sinensis</Emphasis>, the biological control agent of <Emphasis Type="Italic">Dryocosmus kuriphilus</Emphasis> in Italy

A post-release study was performed to assess the impact of Torymus sinensis (Hymenoptera: Torymidae), the biological control agent of Dryocosmus kuriphilus (Hymenoptera: Cynipidae), on native cynipid gall inducers in Italy. In total, 14,512 non-target galls were collected, corresponding to seven genera: Andricus, Aphelonyx, Biorhiza, Cynips, Diplolepis, Neuroterus, and Synophrus, and 8708 chalcid parasitoids were recorded. The Torymidae family accounted for about 30%, and Bootanomyia (=Megastigmus) dorsalis, Torymus affinis and T. flavipes were the most represented species. A total of 116 T. sinensis emerged from 15 different oak galls, mainly Andricus curvator and A. inflator. In controlled conditions, oviposition was recorded on A. cydoniae, A. grossulariae and A. lucidus, while no mating with native congeneric species occurred. This paper confirms the realised host-range expansion by T. sinensis. Even if it were extremely difficult to evaluate its magnitude, the impact appears minimal, and an occasional feeding with no changes in the distribution or abundance of non-target hosts is expected.     

The role of low-penetrance alleles in predisposing the development of sporadic breast cancer

Breast cancer (BC) is one of the most common oncological diseases in the world and has a complex polygenic multifactorial character. The simultaneous analysis of a large number of medium- and low-penetrance genes in the genesis of the sporadic forms of BC makes it possible to more accurately predict the individual risk of this disease, and the analysis of their intergenic associations will help to identify the most significant interactions between several of them. This would significantly simplify further screening studies. In this study, we analyzed all possible combinations of pathogenetically significant polymorphic variants for the key genes involved in (1) repair systems (XRCC1, XRCC3, and PALB2); (2) biotransformation of xenobiotics (NAT2, EPHX1, GSTP1, GSTT1, and GSTM1); (3) cell cycle control (HMMR, TP53); and (4) folate cycle (MTHFR) among patients from Belarus (eastern European region) with the sporadic forms of BC and in the control group. The combinations of genotypes (genetic profile) significantly modifying the risk of sporadic BC were identified using the multifactor dimensionality reduction (MDR). The genetic profile (combinations of genotypes) leading to a significant increase in the risk of sporadic BC is the presence of the G allele in SNP p.I105V (GSTP1), the T allele in SNP p.T241M (XRCC3), and the AA genotype in SNP p.E429A (MTHFR).     

Genome-wide identification and expression profiling analysis of brassinolide signal transduction genes regulating apple tree architecture

Brassinolide (BR) is crucial for regulating plant architecture. Apple dwarfing rootstocks are used to control apple tree size. However, information regarding the effects of BR on apple trees is limited. In addition, the molecular mechanism underlying the dwarfing of apple rootstocks is poorly understood. To elucidate the role of BR signal transduction genes in controlling apple tree architecture, five BR receptor kinase 1 (BRI1), nine BR-signaling kinase 1 (BSK1), two BRI1 KINASE INHIBITOR 1 (BKI1), and seven BR-insensitive 2 (BIN2) genes were analyzed. Bioinformatic analyses revealed that gene duplication events likely contributed to the expansion and evolution of the identified genes. Nine homologs between apple and Arabidopsis thaliana were also identified, and their expression patterns in different tissues were characterized. Exogenous BR treatments increased the primary shoot length and altered the expression of BR signal transduction genes (MdBRI1-5, MdBSK3-8, MdBKI1–2, MdBIN1–4, and MdBIN6/7). The scion of Fuji/Malling 9 (M.9) trees exhibited inhibited growth compared with that of Fuji/Fuji trees. The Fuji/M.9 trees had lower levels of the positive regulators of BR signaling (MdBRI1-5,MdBSK1, MdBSK4/7, and MdBSK6) and higher levels of the negative regulators (MdBIN5-7) compared with the Fuji/Fuji trees. Thus, the above-mentioned genes may help to regulate apple tree size in response to BR. In addition, MdBRI1–5, MdBSK1, MdBSK4/7, MdBSK6, and MdBIN5–7 have important roles in different grafting combinations. Our results may provide the basis for future analyses of BR signal transduction genes regarding their potential involvement in the regulation of plant architecture.     

New sterigmatocystin-producing species of <Emphasis Type="Italic">Aspergillus</Emphasis> section <Emphasis Type="Italic">Versicolores</Emphasis> from indoor air in Croatia

Multilocus DNA sequence-based identification methods raised the number of known species assigned to the Aspergillus section Versicolores. Currently, there are 16 species accepted in the section, including A. amoenus, A. austroafricanus, A. creber, A. cvjetkovicii, A. fructus, A. griseoaurantiacus, A. hongkongensis, A. jensenii, A. protuberus, A. puulaauensis, A. subversicolor, A. sydowii, A. tabacinus, A. tennesseensis, A. venenatus, and A. versicolor. Based on morphological identifications, most of these species were identified as either A. sydowii or A. versicolor, with the latter reported to have a world-wide distribution, growing in many habitats. Aspergillus versicolor has been implicated in health hazards including sick building syndrome, human and animal mycoses, and contamination of food and feed were assigned primarily to this species. A. versicolor is still commonly isolated from indoor surveys, even though species such as A. jensenii and A. creber seem more common. From indoor air samples collected at a grain mill in Croatia, we isolated an undescribed species assigned to the Aspergillus section Versicolores. A polyphasic approach, including sequence-based methods, morphological and physiological studies, was used for species characterization and in this paper is described as Aspergillus pepii. Additionally, sterigmatocystin producing abilities have been confirmed. Based on a combined phylogenetic tree, morphological features and sterigmatocystin producing abilities, A. pepii is closely related to A. versicolor. Further studies should explore the frequency of the species in indoor environments and its medical, industrial, and environmental significance.     

Evolutionary relationships in the genus <Emphasis Type="Italic">Secale</Emphasis> revealed by DArTseq DNA polymorphism

Till this day, there is not much known about the phylogeny of the Secale genus; therefore, in our research, we tried to shed some lights on the issue of rye (Secale genus) taxonomy. The genetic diversity and phylogenetic relationships were evaluated using 13,842 DArTseq? polymorphic markers. The model-based clustering (STRUCTURE software) separated our 84 samples into three main clusters: perennial cluster, annual cluster, and S. sylvestre cluster. The same result was obtained using Neighbour Joining tree and self-organizing maps. Secale sylvestre, S. strictum, and S. cereale are the three main species of the Secale genus. Three samples of rye are in basal positions in phylogenetic trees. These accessions share ancient morphological characters and are probably the ancestors of different lineages within Secale. Annual Secale taxa, with the exception of S. sylvestre, create one mutual taxon. We have found out that the semi-perennial taxa of S. cereale var. multicaule and S. strictum subsp. ciliatoglume are genetically closest to the annual species of S. cereale. Phylogenetic signals for semi-perennial and annual taxa are also present in S. strictum subsp. africanum. SNP-based analysis revealed that evolution of annual S. cereale has already begun in S. strictum subsp. africanum. The results showed that S. vavilovii cannot be considered as a separate species but a subspecies of S. cereale Secale cereale subsp. dighoricum is a hybrid. It is still not clear whether we can consider S. strictum subsp. strictum and S. strictum subsp. kuprijanovii as two separate species.