In silico genomic subtraction guides development of highly accurate, DNA-based diagnostics for Ralstonia solanacearum race 3 biovar 2 and blood disease bacterium

2011 ◽  
Vol 77 (3) ◽  
pp. 182-193 ◽  
Author(s):  
Ryo Kubota ◽  
Mark A. Schell ◽  
Gabriel D. Peckham ◽  
Joanne Rue ◽  
Anne M. Alvarez ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Blood Disease ◽  
Genomic Subtraction

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

scholarly journals PERBANYAKAN IN VITRO PISANG KEPOK var. UNTI SAYANG TAHAN PENYAKIT DARAH MELALUI PROLIFERASI TUNAS

2018 ◽  
Vol 5 (1) ◽  
pp. 36
Author(s):  
Maria Imelda ◽  
Aida Wulansari ◽  
Laela Sari
Keyword(s):  
Ralstonia Solanacearum ◽  
In Vitro Propagation ◽  
Shoot Growth ◽  
Shoot Proliferation ◽  
Shoot Multiplication ◽  
Blood Disease ◽  
Adenine Sulphate ◽  
Banana Variety ◽  
In Vitro Shoot Proliferation

In Vitro Propagation of Kepok Banana var. Unti Sayang Resistant to Blood Disease through Shoot ProliferationABSTRACTKepok is a popular banana variety but sensitive to blood disease caused by Ralstonia solanacearum (Smith). The discovery of a natural mutant of Kepok banana var. Unti Sayang from Sulawesi which male bud falls naturally, is a shortcut to bypass the chains of the spread of blood disease, since the disease is transmitted by insects through the wounds of the male buds. The superior mutant needs to be mass propagated and disseminated to endemic areas to inhibit the spread of blood disease. To achieve that goal, an efficient and effective techniques of in vitro shoot proliferation needs to be developed. Shoot proliferation was performed by addition of BAP, thidiazuron and adenine sulphate. The results showed that the best medium for shoot multiplication was B2T5A (MS+2 mg/L BAP+0,5 mg/L TDZ+20 mg/L adenine sulphate), and for shoot growth was B4A (MS+4 mg/L BAP+20 mg/L adenine sulphate). Rooting was induced on MS medium without hormones. Acclimatization of plantlets on mixed soil, compost and husks with a ratio of 1:1:1 resulted in 92,35% survival rate.Keywords: blood disease, in vitro shoot,  male budless, natural mutant, var. Unti Sayang  ABSTRAKPisang kepok merupakan varietas yang digemari tetapi sangat peka terhadap penyakit darah yang ditimbulkan oleh bakteri Ralstonia solanacearum (Smith). Ditemukannya mutan alami pisang kepok yang jantungnya gugur secara alami yaitu varietas Unti Sayang dari Sulawesi, merupakan jalan pintas untuk memotong rantai penyebaran penyakit darah, mengingat penyakit ini ditularkan oleh serangga melalui luka bekas bunga jantan pada jantung. Mutan unggul tersebut perlu diperbanyak secara massal dan disebarluaskan ke daerah endemik untuk menghambat penyebaran penyakit darah. Untuk mencapai tujuan tersebut, perlu dikembangkan teknik perbanyakan in vitro pisang kepok Unti Sayang yang efektif dan efisien melalui proliferasi tunas. Proliferasi tunas dilakukan dengan penambahan BAP, thidiazuron dan adenin sulfat. Hasil penelitian ini menunjukkan bahwa media terbaik untuk multiplikasi tunas adalah B2T5A (MS+2 mg/L BAP+0,5 mg/L TDZ+20 mg/L adenin sulfat), media terbaik untuk pertumbuhan tunas adalah B4A (MS+4 mg/L BAP+20 mg/L adenin sulfat). Akar dapat diinduksi pada media MS tanpa hormon. Aklimatisasi planlet pada media campuran tanah, kompos dan sekam dengan perbandingan 1:1:1 menghasilkan 92,35% planlet hidup.Kata Kunci: penyakit darah, tunas in vitro, tanpa jantung, mutan alami, var. Unti Sayang 

scholarly journals Analisis Ekspresi Kelompok Gen-Gen Pertahanan Pada Tanaman Pisang Dalam Merespons Bakteri Patogen Ralstonia solanacearum

2018 ◽  
Vol 4 (1) ◽  
pp. 44
Author(s):  
Yunus Effendi ◽  
Arif Pambudi ◽  
Lulu' Nisrina
Keyword(s):  
Real Time ◽  
Ralstonia Solanacearum ◽  
Real Time Pcr ◽  
Post Infection ◽  
Pathogenic Bacteria ◽  
Morphological Data ◽  
Defense System ◽  
Banana Plant ◽  
Musa Paradisiaca ◽  
Blood Disease

<p><em>Abstrak</em> <strong>- </strong><strong><em>Blood Disease Bacterium </em></strong><strong>(BDB) adalah penyakit pada banyak tanaman<em> </em>bernilai ekonomis seperti tanaman pisang yang disebabkan oleh infeksi soil-borne bakteri patogen <em>Ralstonia solanacearum</em>. Kemampuan <em>R.solanacearum</em> untuk bertahan pada kondisi minimum pada tanah dan luasnya spektrum inang pertumbuhannya termasuk vektor perantara, menyebabkan belum ditemukannya strategi efektif untuk menanggulangi penyebaran penyakit BDB. Pengetahuan tentang respons tanaman pisang terhadap serangan <em>Ralstonia solanacearum</em>, merupakan langkah awal untuk memahami stategi tanaman dalam membentuk sistem pertahanan. Dalam penelitian ini, respons ekspresi molekuler gen-gen terkait pertahanan pada tanaman pisang kepok (<em>Musa paradisiaca</em>) dianalisis menggunakan teknik semikuantitatif real time PCR. Data pada penelitian ini menunjukkan <em>WRKY15</em> memiliki penurunan ekspresi pada hari ke-3 dan ke-7 pasca infeksi. <em>WRKY18</em> memiliki ekspresi paling rendah dibandingkan dengan <em>WRKY15 </em>dan<em> WRKY23 </em>serta tidak terdeteksi lagi ekspresinya pada hari ke-5 pasca<em> </em>infeksi karena <em>WRKY18</em> bersifat represi pada pengaturan sistem pertahanan tanaman basal. Level ekspresi <em>WRKY23</em> memiliki pola yang konsisten pada hari ke-1 sampai hari ke-7 pasca infeksi karena <em>WRKY23</em> merupakan salah satu early induced gene. Penelitian ini juga didukung dengan data morfologi yang menunjukkan gejala penyakit layu bakteri berupa penguningan daun pada hari ke-5 pasca infeksi dan pada hari-4 pasca infeksi telah terlihat koloni R.solanacearum pada pseudostem.</strong></p><p> </p><p><strong><em>Kata Kunci </em></strong><em>-<strong> </strong></em><em>Transkriptomik, WRKY, Ralstonia solanacearum, Penyakit Layu<strong> </strong>Bakteri</em></p><p> </p><p><em>Abstract - <strong>Blood Disease Bacterium</strong></em><strong> (BDB) is a disease in many economically valuable plants such as banana plants caused by soil-borne infection of pathogenic bacteria <em>Ralstonia solanacearum</em>. The ability of <em>R. solanacearum</em> to withstand minimum conditions on the ground and the extent of its host growth spectrum including intermediate vectors, has resulted in the lack of effective strategies to combat the spread of BDB. Knowledge about banana plant response to <em>Ranstonia solanacearum</em> attack, is the first step to understand crop strategy in forming defense system. In this study, the response of molecular expression of defense-related genes in banana kepok plant (<em>Musa paradisiaca</em>) was analyzed using semi-quantitative real time PCR technique. Data in this study showed WRKY15 had decreased expression on. WRKY18 has the lowest expression compared to WRKY15 and WRKY23 and no longer detected its expression on the 5th post-infection day because WRKY18 is repressive on the regulation of basal plant defense system. The expression level of WRKY23 has consistent pattern on the 1st day until the 7th post-infection day because WRKY23 is one of the early induced gene. This study was also supported by morphological data showing symptom of bacterial wilt disease in the form of yellowing of leaves on the 5th day post infection and on day 4 post infection has seen colonies R. solanacearum on pseudostem.</strong></p><p><strong> </strong></p><strong><em>Keywords</em></strong><em> - Transcriptomic, WRKY, Ralstonia solanacearum, Blood Disease Bacterium</em>

scholarly journals Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3087-3103 ◽  
Author(s):  
Irda Safni ◽  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
Mark Fegan ◽  
Lindsay Sly ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Type Strain ◽  
Type Species ◽  
Species Complex ◽  
23S Rrna ◽  
Gene Sequences ◽  
Content Type ◽  
Blood Disease ◽  
Link Type ◽  
Ralstonia Pseudosolanacearum

The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S–23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA–DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of Ralstonia solanacearum and consists of strains of R. solanacearum phylotype II only. The second genospecies includes the type strain of Ralstonia syzygii and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely R. syzygii , the causal agent of Sumatra disease on clove trees in Indonesia, R. solanacearum phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of R. solanacearum strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of Ralstonia solanacearum and Ralstonia syzygii and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001T = LMG 10661T = DSM 7385T) for the current R. syzygii strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464T = LMG 27703T = DSM 27478T) for the current R. solanacearum phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627T = LMG 27706T = DSM 27477T) for the BDB strains and Ralstonia pseudosolanacearum sp. nov. (type strain UQRS 461T = LMG 9673T = NCPPB 1029T) for the strains of R. solanacearum phylotypes I and III.

scholarly journals Insects as Carriers of Ralstonia solanacearum Phylotype IV on Kepok Banana Flowers in South Minahasa and Minahasa Districts

2020 ◽  
Vol 13 (1) ◽  
pp. 199-205
Author(s):  
Vivi Montong ◽  
Christina Salaki
Keyword(s):  
Population Density ◽  
Ralstonia Solanacearum ◽  
Sampling Method ◽  
Bacterial Isolates ◽  
Bacterial Isolation ◽  
Blood Disease ◽  
Insect Populations ◽  
Banana Flower ◽  
Insect Sampling ◽  
Insect Collection

The scope of this study is the management of insects that carry the cause of banana blood disease (BBD), Ralstonia solanacearum Phylotype IV. The objectives of this study are: (1) to study the diversity and density of visitor insect populations to the Kepok banana flower, and (2) to identify insects in the Kepok banana flower that act as carriers of R. solanacearum Phylotype IV, and the population density of these bacteria was carried by each insect. Sampling of banana plantations is done based on pusposive sampling method. Insect collection uses a modified insect net, and insect collection uses modified insect nets, and insects were morphologically identified. This bacterial isolation was carried out based on the spread method on NA + TZC media. Inoculation of bacterial isolates was carried out by injection method on the tip of an mature Kepok banana. Density of insects visitors banana flower per tree in South Minahasa and Minahasa regencies are as follows: Oscinella sp. (15.50 and 18.08 individuals), Aphis mellifera (0.50 and 1.58), Chelisoches morio (0.28 and 0.20 individuals, and Dolichoderus sp. (1.44 and 6.21 individuals). All insects on the Kepok banana flower in South Minahasa and Minahasa carry Ralstonia solanacearum Phylotype IV. Oscinella sp., Aphis mellifera, Chelisoches morio, and Dolichoderus sp. in both districts it brought 17,636.39 and 75,533.33 CFU / ml, 15,666.67 and 17,400.00 CFU / ml, 113.33 and 2,667.67 CFU / ml, and 2,400.00 CFU / ml and 21,133.33 CFU / ml.

Sign in / Sign up

Export Citation Format

Share Document