scholarly journals VARIASI INFRASPESIES MACANG (Mangifera foetida) BERDASARKAN SEKUEN GEN rbcL

2019 ◽  
Vol 12 (1) ◽  
pp. 1-7
Author(s):  
Nurul Rafidah ◽  
Fitmawati Fitmawati ◽  
Erwina Juliantari ◽  
Nery Sofiyanti
Keyword(s):  
Maximum Parsimony ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Dna Amplification ◽  
Rapid Decline ◽  
Rbcl Gene ◽  
Neighbor Joining ◽  
Ctab Method ◽  
Nj Tree ◽  
Rbcl Gene Sequences

AbstrakMacang (Mangifera foetida) adalah jenis mangga kosmopolit dengan vigoritas yang kuat. Macang banyak ditemukan di perkarangan dan kebun dan bersifat semi liar. Penurunan luas lahan seperti deforestasi dapat mengakibatkan keanekaragaman kultivar macang juga mengalami penurunan secara cepat. Penelitian ini bertujuan untuk menganalisis dan merekonstruksi hubungan kekerabatan antar kultivar macang menggunakan sekuen gen rbcL. Sampel berasal dari koleksi hasil eksplorasi mangga Sumatera bagian Selatan, yaitu Provinsi Bengkulu, Lampung dan Sumatera Selatan. Ekstraksi DNA dilakukan dengan menggunakan metode CTAB yang dimodifikasi, kemudian DNA diamplifikasi dengan menggunakan primer spesifik rbcL forward dan reverse, dan dilakukan sekuensing serta analisis filogenetik. Rekontruksi pohon filogenetik menggunakan program PAUP* versi 4.0b10 dengan metode Maximum Parsimony (MP) dan Neighbor Joining (NJ). Kladogram dengan MP diperoleh dua klad, yaitu pada klad I terdiri dari kultivar Macang lonjong dan Macang lado, sedangkan klad II terdiri dari kultivar Macang bulat. Berdasarkan metode NJ, diperoleh Macang bulat memiliki jarak genetik lebih panjang sehingga dianggap sebagai individu yang lebih primitif daripada kultivar yang lain. Dengan demikian, dari penelitian ini diperoleh informasi dan bukti dari status taksonomi kultivar macang.Abstract Mangifera foetida is a species of cosmopolitan mango with strong vigor. Some M. foetida are found in some front houses and gardens and has a character of semi-wild in its cultivation. Decreases in land area, such as deforestation, can lead to a rapid decline in their diversity of cultivars. This study aimed to analyze and reconstructs the phylogenetic relationship among M. foetida cultivars using the rbcL gene sequences. Samples were collected from the exploration within the area of South Sumatra, such as Provinces of Bengkulu, Lampung and South Sumatra. The DNA extraction was carried out using the modified CTAB method, followed by DNA amplification using rbcL-specific primers, sequencing, and phylogenetic analysis. The phylogenetic trees were reconstructed using the PAUP* version 4.0b10 by using the method of Maximum Parsimony (MP) and Neighbor Joining (NJ). Cladogram of the MP tree showed two clades that the clad I consisted of M. foetida (Macang lonjong) and M. foetida (Macang lado) cultivars, whereas clad II consisted of M. foetida (Macang bulat) cultivar. The NJ tree showed that M. foetida (Macang bulat) has a longer genetic distance so it is considered as a more primitive cultivar than others. Therefore, information and evidences from the taxonomic status of the M. foetida cultivars were obtained from this study.

Molecular evidence for the systematic positions of two enigmatic mosses: Pterogonidium pulchellum (Sematophyllaceae, Musci) and Piloecium pseudorufescens (Myuriaceae, Musci)

2006 ◽  
Vol 84 (3) ◽  
pp. 501-507
Author(s):  
Ying Chang ◽  
Chan Woon Khiong ◽  
Sean W. Graham ◽  
Benito C. Tan
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Molecular Evidence ◽  
Rbcl Gene ◽  
Branch Support ◽  
New Evidence ◽  
Rbcl Gene Sequences

The systematic position of Pterogonidium pulchellum (W.J. Hooker) Muell. Hal. in the Sematophyllaceae and Piloecium pseudorufescens (Hampe) Muell. Hal. in the Myuriaceae is reexamined with new evidence derived from rbcL gene sequences. A total of 18 taxa from Sematophyllaceae, Hypnaceae, Myuriaceae, and Hookeriaceae were included, 11 of which were newly sequenced for the rbcL gene. Analyses were done using maximum parsimony, maximum likelihood (TrN + Γ + I model and GTR + Γ + I model), and Bayesian inference (GTR + Γ + I model). The results show that Pterogonidium pulchellum has a closer relationship with members of Hypnaceae than with Sematophyllaceae, while Piloecium pseudorufescens forms a clade with the Sematophyllaceae in all phylogenetic analyses, with robust branch support. Two SOWH tests were carried out and the results show that it is not appropriate to classify Pterogonidium pulchellum in Sematophyllaceae and it is also not appropriate to classify Piloecium pseudorufescens in Myuriaceae.

Fritschiella aquatilis (Chaetophoraceae, Chlorophyta), a new freshwater green algae species from China

Phytotaxa ◽  
2019 ◽  
Vol 392 (4) ◽  
pp. 277 ◽  
Author(s):  
HANG SU ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
FANG-RU NAN ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Algal Species ◽  
Taxonomic Status ◽  
Shanxi Province ◽  
Molecular Characteristics ◽  
Rbcl Gene ◽  
Bright Green ◽  
Compensatory Base Changes ◽  
A New Species

A new freshwater algal species of Fritschiella aquatilis was found in a freshwater aquarium in China (Shanxi Province), floating on the surface or sinking at the bottom of the water. This new species is characterized by bright-green, globular thallus with hairy morphology, which composed numerous small single celled filamentous branches. Most characteristics are in agreement with description of Fritschiella. But the new species differs from other members in this genus by the particularly aquatic habitat and macroscopic thalli morphology (the only reported Fritschiella tuberosa Iyengar species is terrestrial). Concatenated sequences from 28S rDNA, 18S rDNA, rbcL gene phylogenetic analysis of F. aquatilis to discuss taxonomic status. All phylogenetic trees have yielded a Fritschiella clade included the sequence, and F. aquatilis formed an independent branch evidently distinguished from other species. Comparing with F. tuberosa, the internal transcribed spacer (ITS) secondary structure of the new species has some compensatory base changes (CBCs) and hemi-CBCs, especially at the Helix1 and Helix 2 end. Thus, the results of morphological and molecular characteristics support F. aquatilis to be recognized as a new species. This new alga brings the total number of recognized Fritschiella species, and the habitats circumscription of the genus Fritschiella expanded to include terrestrial and aquatic.

scholarly journals DNA Isolation And Amplification of the rbcL (ribulose-1,5- bisphosphate carboxylase/oxygenase large subunit) gene of Caulerpa sp., Gracilaria sp., And Sargassum sp.

2020 ◽  
Vol 8 (2) ◽  
pp. 214
Author(s):  
Biondi Tampanguma ◽  
Grevo S. Gerung ◽  
Veibe Warouw ◽  
Billy Th Wagey ◽  
Stenly Wulllur ◽  
...  
Keyword(s):  
Target Gene ◽  
Dna Isolation ◽  
Large Subunit ◽  
Dna Amplification ◽  
Ammonium Bromide ◽  
Rbcl Gene ◽  
Bisphosphate Carboxylase ◽  
Plant Dna ◽  
Ctab Method ◽  
Amplification Process

DNA isolation and gene amplification of algae are significantly influenced by various factors such as characteristics and components of the algae cell wall. Therefore techniques and methods of DNA isolation in certain algae, sometimes only succeed in one particular species and can not be applied to another algae species. Based on that issue, this study was conducted with the aims to determine the succeed of DNA isolation and amplify the rbcL gene as a target gene for identification. Algae DNA was isolated by using innuPrep Plant DNA commercial kit, and the second one with a modified conventional Cetyl Trimetyl Ammonium Bromide (CTAB) method,  for the amplification process was using rbcL gene (ribulose-1,5-bisphosphate carboxylase / oxygenase large subunit) with two pairs of primers : rbcL 7F-753R and rbcL 577F-rbcSR. The results showed that the DNA of Gracilaria sp was succeed isolated by using CTAB method and it was denoted by the presence of DNA bands in agarose gel. Meanwhile DNA amplification for Gracilaria sp., and Sargassum sp., were succeed amplified with the appearance of DNA bands. But in algae Caulerpa sp., was only succeed on 1 pair of primary rbcL 7F and 7.Keywords : DNA, gene rbcL, algae Caulerpa sp., Sargassum sp., Gracilaria sp;AbstrakIsolasi DNA dan amplifikasi gen pada alga sangat dipengaruhi oleh beberapa faktor seperti karakter dan komponen pada dinding sel alga. Oleh karena itu proses isolasi DNA terkadang bisa berhasil pada satu jenis alga, namun tidak berhasil pada jenis alga lainnya. Oleh karena alasan tersebut, maka penelitian ini dilakukan untuk menentukan keberhasilan Isolasi DNA dan mengamplifikasi gen rbcL sebagai gen target identifikasi. Penelitian ini dilakukan dengan tahapan awal Isolasi DNA yang menggunakan kit komersil innuPrep Plant DNA Kit, dan metode konvensional Cetyl Trimetyl Ammonium Bromide (CTAB) yang telah dimodifikasi. Sedangkan untuk proses amplifikasi, menggunakan gen rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) digunakan dua pasang primer yaitu rbcL 7F-753R dan rbcL 577F-rbcSR. Hasil isolasi DNA dari alga Gracilaria sp berhasil diisolasi menggunakan metode CTAB yang ditandai dengan adanya pita DNA pada gel agarose. Amplifikasi DNA pada alga Gracilaria sp., dan Sargassum sp., berhasil diamplifikasi dengan munculnya pita DNA. Namun pada alga Caulerpa sp. hanya berhasil pada 1 pasang primer rbcL 7F dan753R.Kata kunci : DNA, gen rbcL, alga Caulerpa sp., Sargassum sp., Gracilaria sp.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

1994 ◽  
Vol 91 (12) ◽  
pp. 5730-5734 ◽  
Author(s):  
M. Hasebe ◽  
T. Omori ◽  
M. Nakazawa ◽  
T. Sano ◽  
M. Kato ◽  
...  
Keyword(s):  
Rbcl Gene ◽  
Gene Sequences ◽  
Evolutionary Lineages ◽  
Rbcl Gene Sequences

scholarly journals GENETIC IDENTIFICATION OF AQUATIC INVERTEBRATES OF KAZAKHSTAN AS INDICATORS OF ORGANIC POLLUTANTS

2018 ◽  
pp. 139-148
Author(s):  
Alexandr Anatoljevich Volkov ◽  
Larisa Anatoljevna Kovaljova ◽  
Tatjana Timofeevna Troshina ◽  
Zhanara Omirbekovna Mazhibaeva ◽  
Dmitrij Valerjevich Pilin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Aquatic Invertebrates ◽  
Species Abundance ◽  
Ecological Status ◽  
Taxonomic Status ◽  
Organic Pollution ◽  
Water Bodies ◽  
Genetic Identification ◽  
Morphological Identity

The article deals with carrying out DNA barcoding of aquatic invertebrates of Kazakhstan to identify their taxonomic status as organic pollution indicators. 33 species of the Balkhash-Alakol basin and the Zhayik river were analyzed. 21 species correlate (95-100%) with previously published sequences of invertebrates with well-known classifications in the GenBank and BOLD databases. The taxonomic discrepancy in morphometric and genetic parameters in certain species has been revealed. The discrepancy may be caused by the morphological identity in chironomids at a larval stage. The phylogenetic trees of the investigated species within the families Chironomidae and Moinidae have been indicated. Chironomids are represented by ten clades of different types of genetic polymorphism of DNA gene. Genetic links of Moinidae are detected in four groups including a cryptic species from Lake Alakol. It has been stated that in distribution of cryptic taxons in Moina family factors of salinity and depth of the lake are important, as well as differences in depth. Molecular DNA-barcoding of invertebrates of Kazakhstan should be continued with covering a greater number of species and several replications, with qualified primary fixation of subjects of research and a sufficient number of samples. Authenticity of composition defining, species abundance, species characteristics of aquatic invertebrates from the water bodies of poorly explored arid regions is necessary for using them as indicators of the ecological status of water bodies.

scholarly journals Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes

ZooKeys ◽  
2020 ◽  
Vol 975 ◽  
pp. 79-86
Author(s):  
Hai-Jun Yu ◽  
Xiao-Long Lin ◽  
Rui-Lei Zhang ◽  
Qian Wang ◽  
Xin-Hua Wang
Keyword(s):  
Species Delimitation ◽  
Life Stage ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Index Numbers ◽  
Nj Tree ◽  
Barcode Gap

The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.

Molecular Systematics of the Nepetoideae (Family Labiatae): Phylogenetic Implications from rbcL Gene Sequences

1994 ◽  
Vol 49 (9-10) ◽  
pp. 635-645 ◽  
Author(s):  
Martina Kaufmann ◽  
Michael Wink
Keyword(s):  
Rbcl Gene ◽  
Character State ◽  
Specific Primers ◽  
Distance Methods ◽  
Phylogenetic Implications ◽  
Viii And Ix ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rbcl Gene Sequences ◽  
Rbcl Sequences

Abstract Total DNA was extracted from 41 species (20 genera) of the subfamily Nepetoideae (family Labiatae). Using rbcL-specific primers, the rbcL gene was amplified by polymerase chain reaction (PCR) and sequenced directly. RbcL sequences were evaluated with character state (maximum parsimony; PAUP) and distance methods (neighbour-joining; MEGA). In agree­ ment with classical systematics all taxa studied cluster within the Nepetoideae and are clearly distinguished from members of the subfamily Lamioideae. A number of distinctive clades are apparent within the Nepetoideae:, and XIII -Perovskia. At least five main branches rep­ resenting the clades I, II, III to VII, VIII, and IX to XIII respectively, can be distinguished within the Nepetoideae studied. They might be considered representing the tribes (according to Cantino, 1992) Elsholtzieae (I), Lavanduleae (II), and Mentheae (III - XIII). The tribe Mentheae needs to be subdivided into at least three main groups (clades III-VII, VIII and IX -XIII). Major ana hortensis which is often classified as Origanum hortensis does not cluster with Origanum and deserves a generic status of its own.

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