Genetic relationships among loquat cultivars and some wild species of the genus Eriobotrya based on the internal transcribed spacer (ITS) sequences

Genetic relationships were studied among eight species of three taxa in the genus Chaenomeles by nuclear ribosomal internal transcribed spacer (ITS) analysis. A genetic distance matrix based on ITS sequences was estimated according to the formula of Kimura-2 parameter and a neighbour-joining phenogram, which were obtained with Clustalx4.1 software. The results showed that the germplasms of Mugua originate from Ch. speciosa (Sweet) Nakai, not including Ch. sinensis (Thouin) Kochne and Ch. cathayensis (Hemsl.) Schneid. The results also showed that ‘Yao Mugua’ and ‘Ornamental Mugua’ are the most distantly related species in germplasms.

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Group I Intron Versus its Sequences in Phylogeny of Cetrarioid Lichens

The Lichenologist ◽

10.1006/lich.1999.0231 ◽

1999 ◽

Vol 31 (5) ◽

pp. 441-449 ◽

Cited By ~ 9

Author(s):

Arne Thell

Keyword(s):

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Group I Intron ◽

Ribosomal Genes ◽

Its Sequences ◽

Its Sequence ◽

Ribosomal Rna Gene ◽

18S Ribosomal Rna Gene ◽

Group I

AbstractPhylogenetic trees based on group I intron sequences and on internal transcribed spacer (ITS) sequences of mycobiont ribosomal genes were calculated and compared. Eight cetrarioid and four non-cetrarioid species of the Parmeliaceae were compared. The phylogeny based on group I intron sequences is partly congruent with the ITS sequence phylogeny. Group I intron sequences are presumably less informative for infragenic studies. The introns have a length of 214–233 nucleotides, and differ at up to 33% of the bases between species. All introns analysed are located between the positions 1516 and 1517 of the fungal 18S ribosomal RNA gene. Cetrarioid lichens form a non-homogeneous group within the Parmeliaceae according to both group I intron and ITS sequences.

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Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.639 ◽

2020 ◽

Vol 24 (5) ◽

pp. 474-480

Author(s):

I. I. Suprun ◽

S. A. Plugatar ◽

I. V. Stepanov ◽

T. S. Naumenko

Keyword(s):

Genetic Diversity ◽

Bayesian Methods ◽

Dna Markers ◽

Wild Species ◽

Genetic Similarity ◽

Genetic Relationships ◽

Issr Markers ◽

The Other ◽

Clustering Methods ◽

Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

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Application of internal transcribed spacer (ITS) sequences for identifying Anoectochilus setaceus Blume in Thanh Hoa, Vietnam

PROCEEDINGS ON APPLIED BOTANY GENETICS AND BREEDING ◽

10.30901/2227-8834-2020-2-108-116 ◽

2020 ◽

Vol 181 (2) ◽

pp. 108-116

Author(s):

B. B. Thinh ◽

L. D. Chac ◽

L. T.M. Thu

Keyword(s):

Internal Transcribed Spacer ◽

Molecular Taxonomy ◽

Gene Segment ◽

Dna Barcode ◽

Its Sequences ◽

Gene Region ◽

Its Gene ◽

Ctab Method ◽

Young Leaves ◽

Total Dna

Background. The term “DNA barcode” is used extensively in molecular taxonomy. Basically, this technique is based on the use of a DNA sequence (about 400–800 bp) as a standard to identify and determine the species relation of organisms quickly and accurately. Therefore, DNA barcodes not only help taxonomists in classifying and identifying species, but also improve their ability to control, understand and utilize biodiversity. In this study, the authors conducted identification of samples of Anoectochilus setaceus Blume collected in Thanh Hoa through the isolated sequence of ITS gene regions.Materials and methods. Total DNA was extracted from young leaves of A. setaceus samples using CTAB method. The ITS gene segment was amplified by PCR and sequenced. This genetic sequence was analyzed, compared and used to establish a phylogenetic tree using BioEdit, BLAST and DNASTAR programs.Results and conclusion. We isolated 4 sequences of the ITS gene region in 4 A. setaceus samples collected at Xuan Lien and Pu Luong of Thanh Hoa province; the ITS gene region was 667 nucleotide long. The findings identified the samples as the same species and showed 99% similarity to the ITS gene sequence of A. roxburghii (Wall.) Lindl. published in GenBank, GQ328774. This study also demonstrates that the method employing internal transcribed spacer (ITS) sequences is an effective tool to identify A. setaceus taxa.

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A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups

Genome ◽

10.1139/g00-024 ◽

2000 ◽

Vol 43 (3) ◽

pp. 470-476 ◽

Cited By ~ 24

Author(s):

A M Kiers ◽

T HM Mes ◽

R van der Meijden ◽

K Bachmann

Keyword(s):

Wild Species ◽

Genetic Relationships ◽

Group Method ◽

Specific Marker ◽

Pair Group ◽

Cultivar Groups ◽

Average Analysis ◽

Species Analysis ◽

Cultivated Species ◽

Unique Markers

The genus Cichorium consists of two widely cultivated species C. intybus (chicory) and C. endivia (endive) and four wild species, C. bottae, C. spinosum, C. calvum, and C. pumilum. A multivariate and an UPGMA (unweighted pair group method average) analysis based on AFLP (amplified fragment length polymorphism) markers were used to establish the genetic relationships among the species and cultivar groups of C. intybus and C. endivia. At the species level, the results correspond with previously obtained phylogenetic relationships in that C. bottae is the most divergent species, and C. intybus and C. spinosum, as well as C. endivia, C. pumilum, and C. calvum formed clusters. Based on the congruence between phylogenetic and genetic analyses, unique markers were expected for all species, however, hardly any specific marker was found except for C. bottae. The analysis of cultivar groups of C. intybus resembled the species analysis in two respects: (i) grouping of cultivars according to cultivar groups, and (ii) lack of markers unique to cultivar groups. In contrast to C. intybus, the cultivar series of C. endivia do not form distinct groups, which would reflect that crosses have been made among the various cultivar groups. The relationships among Cichorium species and cultivars will be useful for setting up a core collection of Cichorium, and stress the importance of inclusion of the wild species in the collection.Key words: Cichorium, AFLP, diagnostic markers, cultivar relationships, genetic resources.

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Genetic relationships among isolates of Phoma ligulicola from pyrethrum and chrysanthemum based on ITS sequences and its detection by PCR

Australasian Plant Pathology ◽

10.1071/ap03097 ◽

2004 ◽

Vol 33 (2) ◽

pp. 173 ◽

Cited By ~ 16

Author(s):

S. J. Pethybridge ◽

J. B. Scott ◽

F. S. Hay

Keyword(s):

Genetic Relationships ◽

Its Sequences

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First Report of Colletotrichum boninense Causing Anthracnose on Pepper in China

Plant Disease ◽

10.1094/pdis-04-12-0403-pdn ◽

2013 ◽

Vol 97 (1) ◽

pp. 138-138 ◽

Cited By ~ 7

Author(s):

Y. Z. Diao ◽

J. R. Fan ◽

Z. W. Wang ◽

X. L. Liu

Keyword(s):

Internal Transcribed Spacer ◽

Severe Disease ◽

Causal Agent ◽

Its Sequences ◽

Universal Primers ◽

Pathogenicity Test ◽

Conidial Suspension ◽

Single Spore ◽

First Report ◽

Species Specific

Anthracnose, caused by Colletotrichum spp., is a severe disease and results in large losses in pepper (Capsicum frutescens) production in China (4). Colletotrichum boninense is one of the Colletotrichum species in pepper in China. In August 2011, anthracnose symptoms (circular, sunken lesions with orange to black spore masses) were observed on pepper fruits in De-Yang, Sichuan Province, China. Three single-spore isolates (SC-6-1, SC-6-2, SC-6-3) were obtained from the infected fruits. A 5-mm diameter plug was transferred to potato dextrose agar (PDA); the isolates formed colonies with white margins and circular, dull orange centers. The conidia were cylindrical, obtuse at both ends, and 10.5 to 12.6 × 4.1 to 5.0 μm. The colonies grew rapidly at 25 to 28°C, and the average colony diameter was 51 to 52 mm after 5 days on PDA at 25°C. Based upon these characters, the causal agent was identified as C. boninense. To confirm the identity of the isolates, the internal transcribed spacer (ITS) regions were amplified with the ITS1/ITS4 universal primers (1). The internal transcribed spacer (ITS) sequences (Accession No. JQ926743) of the causal fungus shared 99 to 100% homology with ITS sequences of C. boninense in GenBank (Accession Nos. FN566865 and EU822801). The identity of the causal agent as C. boninense was also confirmed by species-specific primers (Col1/ITS4) (2). In a pathogenicity test, five detached ripe pepper fruits were inoculated with 1 μl of a conidial suspension (106 conidia/mL) or five fruits with 1 μl of sterile water were kept as control. After 7 days in a moist chamber at 25°C, typical anthracnose symptoms had developed on the five inoculated fruits but not on control fruits. C. boninense was reisolated from the lesions, and which was confirmed by morphology and molecular methods as before. There have reports of C. boninense infecting many species of plants, including pepper (3). To our knowledge, this is the first report of C. boninense causing anthracnose on pepper in China. References: (1) A. K. Lucia et al. Phytopathology 93:581, 2002. (2) S. A. Pileggi et al. Can. J. Microbiol. 55:1081, 2009. (3) H. J. Tozze et al. Plant Dis. 93:106, 2009. (4) M. L. Zhang. J. Anhui Agri. Sci. 2:21, 2000.

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Research Article ISSR and SSR markers for determining genetic relationships among three wild species of Passiflora

Genetics and Molecular Research ◽

10.4238/gmr18040 ◽

2019 ◽

Vol 18 (1) ◽

Author(s):

L.S. Vianna ◽

T.N.S. Pereira ◽

E.A. Santos ◽

A.P. Viana ◽

M.G. Pereira ◽

...

Keyword(s):

Ssr Markers ◽

Wild Species ◽

Genetic Relationships ◽

Research Article

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CONTRIBUTIONS TO THE KNOWLEDGE OF CAMBODIAN CYPERACEAE

Edinburgh Journal of Botany ◽

10.1017/s0960428619000015 ◽

2019 ◽

Vol 76 (2) ◽

pp. 197-220

Author(s):

K. Tremetsberger ◽

S. Hameister ◽

D. A. Simpson ◽

K.-G. Bernhardt

Keyword(s):

Phylogenetic Analysis ◽

Southeast Asia ◽

Phylogenetic Tree ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Sequences ◽

Cryptic Variation ◽

The Family ◽

History Of ◽

Rapid Radiations

To date, there are very few sequence data for Cyperaceae from mainland Southeast Asia. The aim of the present study was to contribute nuclear ribosomal internal transcribed spacer (ITS) sequences of selected species of Cambodian Cyperaceae to the overall phylogeny of the family. We generated ITS sequences of 38 accessions representing 26 species from Cambodia and used these sequences for phylogenetic analysis together with similar sequences from the National Center for Biotechnology Information GenBank. Our results corroborate recent phylogenetic work in the family and largely confirm established tribal relationships. The backbone of the phylogenetic tree of species-rich genera that have undergone rapid radiations is often weakly resolved (e.g. in Fimbristylis and in the C4 clade of Cyperus). Cryptic variation was revealed in the taxonomically difficult group of Fimbristylis dichotoma, with samples of this taxon appearing in two distinct clades within Fimbristylis. Further addition of geographically spread accessions of taxa will improve our understanding of the complex biogeographical history of the genera in the family. Eleocharis koyamae Tremetsb. & D.A.Simpson is proposed as a new name for E. macrorrhiza T. Koyama.

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Three novel species of Russula from southern China based on morphological and molecular evidence

Phytotaxa ◽

10.11646/phytotaxa.392.4.2 ◽

2019 ◽

Vol 392 (4) ◽

pp. 264 ◽

Cited By ~ 3

Author(s):

JING-WEI LI ◽

JIAN-FEI ZHENG ◽

YU SONG ◽

FA YUAN ◽

LI-HONG QIU

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Internal Transcribed Spacer ◽

Novel Species ◽

Southern China ◽

Morphological Characters ◽

Its Sequences ◽

Molecular Evidence ◽

Three New Species

Three new species of Russula collected from southern China are proposed based on morphological characters and phylogenetic analysis of internal transcribed spacer (ITS) sequences. Russula bubalina sp. nov. is characterized by cinnamon buff to pink pileus with striate margin, interveined and forked lamellae, basidiospores with warty ornamentations not forming reticulum, hymenial cystidia becoming brown in sulphovanillin (SV) and slender terminal cells in suprapellis. R. pseudobubalina sp. nov. is closely related to Russula bubalina in macro-morphology, but it can be recognized by its unforked lamellae, shorter cheilocystidia, bigger basidia and basidiospores with lower ornamentations. Russula subatropurpurea sp. nov. can be recognized by the purplish brown pileus, mild-tasted and white context changing to light purplish red with FeSO4, white and forking lamellae without lamellulae, long hymenial cystidia becoming brown in SV. Both morphological and phylogenetic analysis consistently confirmed the distinct positions of three new species in subg. Heterophyllidia subsection Heterophyllinae.

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