Genetic diversity of Peucedanum japonicum using Internal Transcribed Spacer (ITS) sequence

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.

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Identification and genetic diversity of Acer ibericum (Aceraceae) in South Caucasus

Journal of Forest Science ◽

10.17221/36/2021-jfs ◽

2021 ◽

Vol 67 (No. 9) ◽

pp. 420-426

Author(s):

Juraj Paule ◽

Nani Goginashvili ◽

Irina Tvauri ◽

Ladislav Paule ◽

Ekaterine Gabashvili ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Marker ◽

Internal Transcribed Spacer ◽

Population Genetic ◽

National Park ◽

Its Sequence ◽

South Caucasus ◽

Conservation Measures

Internal transcribed spacer (ITS) sequence was tested in Acer ibericum for its suitability as a barcoding as well as population genetic marker. The marker was reliably used to identify A. ibericum as well as to gain preliminary insights into the genetic diversity of Georgian populations. MegaBLAST searches of studied samples against the GenBank database revealed that all studied accessions could be considered Acer ibericum. Populations from Vashlovani National Park revealed the presence of unique ribotypes, and together with the population from Shavi Mountain, they were identified as the most genetically diverse ones. Based on presented data the populations from Eastern Georgia should be prioritized if conservation measures are planned.

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Genetic diversity of Rhizopus microsporus from traditional inoculum of tempeh in Indonesia based on ITS sequences and RAPD marker

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200331 ◽

2019 ◽

Vol 20 (3) ◽

pp. 847-852

Author(s):

TATI BARUS ◽

RONALDO HALIM ◽

ANASTASIA TATIK HARTANTI ◽

PAULUS KEVIN SAPUTRA

Keyword(s):

Genetic Diversity ◽

Internal Transcribed Spacer ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Its Sequences ◽

Its Sequence ◽

Rhizopus Microsporus ◽

Universal Primer ◽

Cluster 2

Abstract. Barus T, Halim R, Hartanti AT, Saputra PK. 2019. Genetic diversity of Rhizopus microsporus from traditional inoculum of tempeh in Indonesia based on ITS sequences and RAPD marker. Biodiversitas 20: 847-852. The main microorganism for tempeh fermentation is Rhizopus microsporus. These days, many tempeh producers use commercial inoculum, such as ‘Raprima’ as resource of R. microsporus. As a result, the genetic diversity of R. microsporus that had been reported in Indonesia has diminished. Information about genetic diversity is needed as a basis to select R. microsporus as tempeh inoculum. This research aims to investigate the genetic diversity of R. microsporus from waru leaves based on Internal Transcribed Spacer (ITS) Sequence and Random Amplified Polymorphic DNA (RAPD) markers. A total of 25 R. microsporus were isolated from traditional inoculum waru leaves (Inoculum 1) and traditional inoculum other than waru leaves (Inoculum 2). Amplification of ITS sequence was done using universal primer pairs of ITS-4 and ITS-5. Amplification of RAPD markers was done using primers OPC-08, OPC-19, OPQ-6, R-108, OPA-09 and OPJ-20. ITS sequence was not sufficient to compare the similarities among R. microsporus. On the other hand, RAPD markers successfully compared the similarities among 25 R. microsporus. A total of 25 R. microsporus were divided into 9 clusters. R. microsporus from Inoculum 1 grouped into Cluster 1, Cluster 3 and Cluster 4-8. Inoculum 2 grouped into Cluster 2 and Cluster 9. R. microsporus from tempeh grouped into Cluster 4 and was different from Inoculum 1 and Inoculum 2, except for TB3.

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Higher-level relationships among the eucalypts are resolved by ITS-sequence data

Australian Systematic Botany ◽

10.1071/sb00039 ◽

2002 ◽

Vol 15 (1) ◽

pp. 49 ◽

Cited By ~ 82

Author(s):

Dorothy A. Steane ◽

Dean Nicolle ◽

Gay E. McKinnon ◽

René E. Vaillancourt ◽

Brad M. Potts

Keyword(s):

Internal Transcribed Spacer ◽

Sequence Data ◽

Its Region ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

Its Sequence ◽

Phylogenetic Groups ◽

Single Section ◽

Western Australian ◽

Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

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WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

The Scientific World JOURNAL ◽

10.1100/2012/689296 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Victor Olusegun Oyetayo

Keyword(s):

Sequence Analysis ◽

Phylogenetic Tree ◽

Molecular Identification ◽

Internal Transcribed Spacer ◽

Its Region ◽

Its Sequence ◽

African Countries ◽

African Species ◽

Its Sequence Analysis ◽

Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

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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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Phylogenetic analysis of Mexican and Central American Pinguicula (Lentibulariaceae) based on internal transcribed spacer (ITS) sequence

Chromosome Botany ◽

10.3199/iscb.2.67 ◽

2007 ◽

Vol 2 (2) ◽

pp. 67-77 ◽

Cited By ~ 4

Author(s):

Hiro Shimai ◽

Katsuhiko Kondo

Keyword(s):

Phylogenetic Analysis ◽

Internal Transcribed Spacer ◽

Central American ◽

Its Sequence

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Genetic Diversity and Origin of Siam Weed (Chromolaena odorata) in Australia

Weed Technology ◽

10.1017/s0890037x00042524 ◽

1998 ◽

Vol 12 (1) ◽

pp. 27-31 ◽

Cited By ~ 13

Author(s):

Leon J. Scott ◽

Corinna L. Lange ◽

Glenn C. Graham ◽

David K. Yeates

Keyword(s):

Genetic Diversity ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Southern Brazil ◽

Chromolaena Odorata ◽

Base Pairs ◽

Its1 Sequence ◽

Its1 Region ◽

Native And Introduced Ranges ◽

The U.S

Asynchronous flowering was noted in a recently discovered infestation of siam weed in north Queensland. This may indicate some genetic diversity in the infestation, increasing concerns about the origin of the infestation. Internal transcribed spacer 1 (ITS1) sequence data were obtained for siam weed individuals from north Queensland, Indonesia, Thailand, South Africa, Ivory Coast, Brazil, Colombia, and the U.S. The ITS1 region is 258 base pairs long, and the populations that flower at different times in north Queensland differ by four base substitutions. The genotype common in north Queensland is also reported throughout the native and introduced ranges. The other genotype is reported only in north Queensland and southern Brazil. These data, in conjunction with prior investigations into possible origins, indicate that Brazil is the most likely source of the infestation in Australia.

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