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Abstrak :
Aspergillus section Nigri adalah salah satu kelompok kapang yang memiliki peran penting dalam bidang mikologi pangan, kedokteran, dan bioteknologi. Kapang tersebut merupakan kandidat yang sering digunakan untuk rekayasa genetika dan pemerintah Amerika Serikat melalui Food and Drug Administration (FDA) memberikan status GRAS (Generally Regarded As Safe) dalam penggunaannya di bidang industri dan bioteknologi. Secara sistematika dan taksonomi, kapang Aspergillus section Nigri memiliki sejumlah permasalahan karena kapang tersebut sukar untuk diidentifikasi dan diklasifikasi. Dalam penelitian ini dilakukan identifikasi dan analisis filogenetik terhadap 20 strain Aspergillus section Nigri terseleksi asal Kebun Raya Eka Karya, Bedugul Bali. Identifikasi kapang terseleksi dilakukan melalui pendekatan morfologi dan molekuler. Karakterisasi morfologi dilakukan dengan mengamati karakter fenotip di media CzA, MEA, CYA, MEA37, dan CY20S. Adapun analisis molekuler dilakukan melalui analisis sekuensing gen pada lokus ITS rDNA, gen ß-tubulin dan calmodulin. Analisis filogenetik dilakukan menggunakan analisis statistik neighbor-joining (NJ). Hasil analisis morfologi dalam penelitian ini belum dapat digunakan untuk mengidentifikasi dan membedakan ke-20 strain pada tingkat takson spesies. Hasil analisis molekuler menunjukkan 7 strain memiliki kedekatan secara genotip dengan A. aculeatus pada kisaran homologi 97-99%, 4 strain memiliki kedekatan dengan A. niger pada kisaran homologi 99-100%, dan 9 strain memiliki kedekatan genotip dengan A. tubingensis pada kisaran homologi 97-100%. Hasil analisis molekuler juga menunjukkan 10 strain yaitu P03, P08, P09,P10, P12, P15, P16, P18, P19, dan P20 memiliki homologi yang rendah pada lokus gen ß-tubulin dan calmodulin sehingga secara genotip strain tersebut kemungkinan merupakan kandidat spesies yang berbeda. Hasil tersebut diperkuat oleh hasil analisis filogenetik NJ pada ketiga lokus. Berdasarkan hasil analisis filogenetik multilokus strain P01, P02, P11, dan P17 adalah takson A. tubingensis, strain P04, P05, P06, dan P07 adalah takson A. niger, dan strain P13 dan P14 adalah takson A. aculeatus. Hasil analisis filogenetik juga menunjukkan adanya spesies tersembunyi (cryptic species) dari beberapa strain Aspergillus hitam yang disolasi dari rhizosfer Piper asal Kebun Raya Eka Karya, Bedugul Bali, yaitu strain P03, P08, P09, P10, P12, P15, P16, P18, P19, dan P20. ......The black aspergilli (Aspergillus section Nigri ) are an important group of species in food mycology, medical mycology, and biotechnology. They are also candidates for genetic manipulation in the biotechnolology industries since A. niger used under certain industrial condition has been granted the GRAS (Generally Regarded As Safe) status by the Food and Drug Administration of the US government. Black aspergilli are one of the more difficult groups regarding classification and identification. In spite of the taxonomy of the Aspergillus species of the Nigri section being regarded as troublesome. This work aimed to identify and analyse the phylogeny of 20 selected strains of black aspergilli from Eka Karya Botanical Garden, Bedugul Bali. Morphological character were observed from culture were grown on CzA, MEA, CYA, MEA37, and CY20S. Meanwhile, molecular analysis have been conducted based on the ITS rDNA, ß-tubulin, and calmodulin genes. Morphological data result are useful for preliminary identification but it did not having been totally effective in describing and elucidating 20 selected strains into species level. Further molecular analysis showed that from 20 selected strains, seven strains have 97-99% similarity with A. aculeatus, four strains have 99-100% similarity with A. niger, and nine strains have 97-100% similarity with A. tubingensis. Based on molecular analysis particularly ß-tubulin and calmodulin genes, 10 strains (P03, P06, P08, P09, P10, P12, P15, P16, P18, P19, and P20) can be presumed as new species because of the low homology value to their closest related species. Based on the phylogenetic analysis strains of P01, P02, P11, and P17 were identified as A. tubingensis; strain P04, P05, P06, and P07 were identified as A. niger, and strain P13 and P14 were identified as A. aculeatus. Ten strains, namely, P03, P08, P09, P10, P12, P15, P16, P18, P19, and P20, form distinct lineage separated from other recognized Aspergillus in this section. Cryptic species probably exist among the Aspergillus section Nigri strains inhabiting Piper rhizosphere from Eka Karya Botanical Garden, Bedugul Bali.

Abstrak :
ABSTRAK
Penelitian bertujuan menganalisis hubungan kekerabatan spesies-spesies Cercospora berdasarkan data sequence daerah Internal Transcribed Spacers (ITS) rDNA, gen elongation factor 1-α (EF), dan gen calmodulin (CAL); mengetahui lokus yang paling baik dalam memisahkan spesies-spesies Cercospora; dan menguji host specificity Cercospora spp. dengan tanaman inangnya. Pada penelitian ini telah dilakukan amplifikasi dan sequencing daerah ITS rDNA, gen EF, dan gen CAL pada 14 spesies dari 23 strain Cercospora yang berasal dari tiga famili tanaman inang (Asteraceae, Cucurbitaceae, dan Solanaceae). Pohon filogenetik dibangun menggunakan metode Neighbor-Joining, Maximum Parsimony, dan Bayesian. Hasil penelitian menunjukkan bahwa pohon filogenetik berdasarkan data sequence daerah ITS rDNA tidak dapat menjelaskan hubungan kekerabatan antarspesies pada genus Cercospora; sebagian besar Cercospora (57 dari 61 OTU) berada dalam satu kelompok besar yang jarak cabangnya berimpit satu dengan lainnya. Pohon filogenetik berdasarkan data sequence gen EF dapat menjelaskan hubungan kekerabatan beberapa spesies Cercospora, walaupun sebagian spesies Cercospora (24 OTU) berada dalam satu kelompok yang jarak cabangnya berimpit satu dengan lainnya. Pohon filogenetik berdasarkan data sequence gen CAL dapat menjelaskan hubungan kekerabatan sebagian besar spesies Cercospora, jarak cabang terlihat lebih panjang dibandingkan pada pohon filogenetik berdasarkan data sequence gen EF, walaupun beberapa spesies Cercospora (16 OTU) belum dapat dipisahkan. Hasil analisis filogenetik menunjukkan bahwa spesies-spesies Cercospora tidak dapat dipisahkan berdasarkan data sequence daerah ITS rDNA, akan tetapi sebagian spesies dapat dipisahkan berdasarkan data sequence gen EF dan gen CAL. Pohon filogenetik berdasarkan data sequence gen CAL menunjukkan bahwa gen tersebut dapat digunakan untuk memisahkan spesies-spesies Cercospora lebih baik daripada daerah ITS rDNA dan gen EF. Hasil analisis filogenetik berdasarkan data sequence multilokus menunjukkan bahwa 11 dari 14 spesies Cercospora yang digunakan dalam penelitian tidak host-specific, hanya tiga spesies yaitu C. zinniicola, C. cocciniae, dan C. mikaniicola yang spesifik terhadap inangnya.

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ABSTRACT
The aims of this study were to analyze the phylogenetic relationships of Cercospora spp. based on sequence data of the internal transcribed spacer (ITS) region of rDNA, elongation factor 1-α (EF), and calmodulin (CAL) genes; to determine the best locus in separating Cercospora species; and to investigate the host specificity of Cercospora spp. In this study, the sequences of the ITS region of rDNA, EF, and CAL genes of 23 strains which belong to 14 species of Cercospora from three host plants families were amplified and sequenced. The phylogenetic trees of the Cercospora spp. were constructed by Neighbor-Joining, Maximum Parsimony, and Bayesian methods. Our result showed that phylogenetic relationship of Cercospora at the species level could not be resolved by ITS rDNA; most of Cercospora species (57 OTU) were grouped in one major clade with no branch length differences among species. The EF phylogenetic tree, showed that some species of Cercospora could be separated, although 24 OTU were grouped into one clade with no branch length differences. The CAL phylogenetic tree showed that the majority of Cercospora species could be separated with longer branch compared to the EF phylogenetic tree, although several species (16 OTU) could not be separated. The phylogenetic analyses showed that most of Cercospora species could not be separated in the ITS rDNA tree, however those species could be separated in the EF and CAL phylogenetic trees. The results showed that CAL gene was the best locus in separating Cercospora species compared to ITS rDNA and EF gene. Molecular phylogenetic analysis from multiloci (ITS regions of rDNA, EF gene, and CAL gene) revealed that 11 out of 14 species of Cercospora have no host specificity (have a wide host range) and only three species e.g., C. zinniicola, C. cocciniae, and C. mikaniicola showed host specificity.