scholarly journals Variasi Gen matK dan Filogenetik Tumbuhan Kantong Semar (Nepenthes sp.) dari Gunung Mahawu dan Gunung Soputan di Sulawesi Utara (The Variation of matK Gene and the Phylogeny of Nepenthes sp. Obtained from Mount Mahawu and Mount Soputan in North Sulawesi)

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Jenifer Tambuwun ◽  
Beivy J Kolondam ◽  
Trina E Tallei
Keyword(s):  
Gene Sequence ◽  
Forest Conversion ◽  
Nucleotide Difference ◽  
Pitcher Plant ◽  
North Sulawesi ◽  
As Species ◽  
Matk Gene ◽  
Base Analysis ◽  
Protected Plants ◽  
Barcode Gap

Abstrak Kantong semar (Nepenthes sp.) merupakan salah satu tumbuhan langka yang dilindungi. Eksploitasi yang berlebihan, serta alih fungsi hutan menjadi ancaman bagi kehidupan Nepenthes sp. Penelitian ini bertujuan untuk menentukan variasi gen matK dari tumbuhan Nepenthes sp. di Gunung Mahawu (JTM) dan Gunung Soputan (JTS) di Sulawesi Utara dan membandingkannya dengan kerabat terdekat di GenBank, serta membuat pohon filogenetiknya. Hasil penelitian menunjukkan bahwa hanya terdapat satu perbedaan nukleotida sekuens gen matK antara Nepenthes sp. dari Gunung Mahawu dan Gunung Soputan. Selain itu, variasi juga ditunjukan pada Nepenthes sp. yang diperoleh dari basis data GenBank dengan adanya perbedaan 1-7 basa nukleotida dengan sampel penelitian ini. Hasil analisis menggunakan ABGD (Automatic Barcode Gap Discovery) menunjukkan bahwa variasi intraspesies untuk Nepenthes sp. berada dalam rentang 0,000 – 0,004. Apabila mempertimbangkan barcode gap tersebut sebagai pembatas spesies, maka diasumsikan bahwa JTM, JTS, N. fusca, N. pilosa, N. maxima, N. faizaliana, dan N. clipeata merupakan spesies yang sama. Hal ini ditunjang oleh rekonstruksi pohon filogenetik menggunakan gen matK.Kata Kunci: ABGD, barcode gap, gen matK, Nepenthes sp., pohon filogenetik, variasi sekuens. Abstract Tropical pitcher plant (Nepenthes sp.) is listed as one of the endangered and protected plants. Excessive exploitation and forest conversion threaten the life of this Nepenthes sp. This research was aimed to determine variation in matK gene of Nepenthes sp. obtained from Mount Mahawu (JTM) and Mount Soputan (JTS) North Sulawesi, and compare the matK sequences with their allied taxa in public domain data base. Analysis of matK gene showed that there was only one nucleotide difference of matK gene sequence between Mahawu and Soputan samples. There were 1-7 different nucleotides between those samples and their allied taxa. Analysis of barcode gap using ABGD (Automatic Barcode Gap Discovery) showed that the range of intraspecies variation of Nepenthes sp. was 0,000 – 0,004. Considering this barcode gap generated from ABGD as species delimination, it could be assumed that JTM, JTS, N. fusca, N. pilosa, N. maxima, N. faizaliana, dan N. clipeata were the same species. These results were also supported by the reconstruction of phylogenetic tree using matK gene.Keywords: ABGD, barcode gap, matK gene, Nepenthes sp., phylogeneteic tree, sequence variation. 

scholarly journals Variasi Genetik Troides helena (Lepidoptera: Papilionidae) Berdasarkan Gen COI (Cytochrome C Oxydase I)

Jurnal MIPA ◽  
2015 ◽  
Vol 4 (2) ◽  
pp. 141
Author(s):  
Claudius F. Kairupan ◽  
Roni Koneri ◽  
Trina E. Tallei
Keyword(s):  
Genetic Variation ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Gene Sequence ◽  
Forest Conversion ◽  
Butterfly Species ◽  
Cytochrome C Oxidase I ◽  
Nucleotide Difference ◽  
Remote Locations ◽  
Gene Sequence Analysis

Kupu-kupu Troides helena (Kupu-kupu Raja) merupakan salah satu spesies langka yang dilindungi. Eksploitasi yang berlebihan, serta alih fungsi hutan menjadi ancaman bagi kehidupan kupu-kupu ini. Penelitian ini dilakukan untuk mengetahui variasi  pada gen cytochrome C oxidase I Troides helena yang diperoleh dari dua lokasi yang berbeda, yaitu Gunung Tumpa dan Gunung Dua-sudara. Analisis sekuens menunjukkan adanya perbedaan satu pasang basa nukleotida dari kedua spesimen tersebut.  Selain itu, variasi juga ditunjukan pada sampel yang diperoleh dari basis data GenBank dengan adanya perbedaan 7-8 pasang basa nukleotida dengan  spesimen pada penelitian ini. Hasil perhitungan jarak genetik menunjukkan bahwa meskipun secara geografis spesimen-spesimen uji ini berasal dari lokasi yang berjauhan, variasi genetik masih berada dalam kisaran variasi intraspesies.Troides helena (Common Birdwing) is listed as one of endangered and protected butterfly species. Excessive exploitation and forest conversion have become threat to the life of this butterfly. This study was conducted to determine the genetic variation of Troides helena obtained from Mt. Tumpa and Mt. Dua-sudara based on cytochrome C oxidase I gene. Sequence analysis shows one nucleotide difference between these two specimens. Moreover, genetic variation also has been shown by comparing these two specimen with other Troides helena obtained from database in GenBank. There are 7-8 nucleotides differences among tested specimens. The result of genetic distance calculations indicates that although geographically these test specimens derived from remote locations, the genetic variation is still within the range of intraspecific variation.

The reassignment of three ‘lost’ Taphrina species (Taphrina bullata, Taphrina insititiae and Taphrina rhizophora) supported by the divergence of nuclear and mitochondrial DNA

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3091-3098 ◽  
Author(s):  
Jana Petrýdesová ◽  
Kamila Bacigálová ◽  
Pavol Sulo
Keyword(s):  
Vascular Plants ◽  
Type Strain ◽  
Gene Sequence ◽  
Ribosomal Subunit ◽  
Sequence Divergence ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
As Species ◽  
Morphological And Physiological Traits ◽  
26S Rrna

The ascomycetous genus Taphrina Fries originally contained more than 90 phytopathogenic microscopic dimorphic ascomycetes causing specific infections in different vascular plants. Although species have mainly been identified historically according to their host and morphological and physiological traits, they can be studied and preserved in the form of yeasts arising from germinating ascospores. Due to low DNA sequence divergence and the lack of available strains, the number of accepted Taphrina species has currently been reduced to 28. The aim of this study is the description of three previously accepted species. Taphrina bullata (type strain CCY 58-4-1 = CBS 12783), Taphrina insititiae (type strain CCY 58-5-1 = CBS 12782) and Taphrina rhizophora (type strain CCY 58-6-1 = CBS 12781), which have been omitted from a recent key. The host range, the divergence of the 26S rRNA gene sequence, internal transcribed spacers (ITS) and the mitochondrial small ribosomal subunit (rns) sequence strongly support their reassignment as species.

Molecular systematics in the genus Clintonia and related taxa based on rbcL and matK gene sequence data

2001 ◽  
Vol 16 (2) ◽  
pp. 119-137 ◽  
Author(s):  
Kazuhiko Hayashi ◽  
Seiji Yoshida ◽  
Frederick H. Utech ◽  
Shoichi Kawano
Keyword(s):  
Molecular Systematics ◽  
Gene Sequence ◽  
Sequence Data ◽  
Matk Gene ◽  
Gene Sequence Data

scholarly journals The matK gene: sequence variation and application in plant systematics

1997 ◽  
Vol 84 (6) ◽  
pp. 830-839 ◽  
Author(s):  
Khidir W. Hilu ◽  
gping Liang
Keyword(s):  
Sequence Variation ◽  
Gene Sequence ◽  
Plant Systematics ◽  
Matk Gene

scholarly journals Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.

2006 ◽  
Vol 56 (7) ◽  
pp. 1599-1605 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Yoshimi Benno
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
As Species ◽  
Gene Sequence Analysis ◽  
Chemotaxonomic Characteristic ◽  
Tannerella Forsythensis ◽  
Type Strains

The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, Parabacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, Parabacteroides distasonis gen. nov., comb. nov. (the type species), Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.

scholarly journals Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae)

ZooKeys ◽  
2021 ◽  
Vol 1036 ◽  
pp. 121-151
Author(s):  
Jia-Jun He ◽  
Du-Ting Jin ◽  
Yi-Shu Wang ◽  
Yan-Li Che ◽  
Zong-Qing Wang
Keyword(s):  
New Species ◽  
Confidence Interval ◽  
Genetic Distance ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Operational Taxonomic Units ◽  
As Species ◽  
The Difference ◽  
Morphological Differences ◽  
Barcode Gap

Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He & Z-Q Wang, sp. nov., Margattea cuspidata J-J He & Z-Q Wang, sp. nov., Margattea caudata J-J He & Z-Q Wang, sp. nov., Margattea paratransversa J-J He & Z-Q Wang, sp. nov., Margattea disparilis J-J He & Z-Q Wang, sp. nov., Margattea transversa J-J He & Z-Q Wang, sp. nov., and Margattea bicruris J-J He & Z-Q Wang, sp. nov.

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