scholarly journals The genome sequence of hairy root Rhizobium   rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Marjolein J. G. Hooykaas ◽  
Paul J. J. Hooykaas
Keyword(s):  
Genome Sequence ◽  
Hairy Root ◽  
Bioinformatics Analysis ◽  
Ri Plasmid ◽  
Rhizobium Rhizogenes

scholarly journals The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402. Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid

2021 ◽  
Author(s):  
Marjolein Hooykaas ◽  
Paul Hooykaas
Keyword(s):  
Genome Sequence ◽  
Hairy Root ◽  
Complete Genome ◽  
Dynamic Nature ◽  
Ri Plasmid ◽  
Ti Plasmids ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Rhizobium Rhizogenes ◽  
Biocontrol Strain

We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. In order to assemble a complete genome we obtained short-reads from Illumina sequencing as well as long-reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL-region that has the signature of a new opine catabolic gene cluster including the three genes that together encode an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.

scholarly journals Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt

Gene ◽  
2021 ◽  
Vol 769 ◽  
pp. 145237
Author(s):  
Mahmoud ElHefnawi ◽  
Elsayed Hegazy ◽  
Asmaa Elfiky ◽  
Yeonsu Jeon ◽  
Sungwon Jeon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bioinformatics Analysis ◽  
Clinical Information ◽  
Geographic Regions

scholarly journals Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834

2014 ◽  
Vol 2 (5) ◽  
Author(s):  
K. Kajala ◽  
D. A. Coil ◽  
S. M. Brady
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Strain Atcc ◽  
Rhizobium Rhizogenes

scholarly journals Kultur akar rambut Cinchona ledgeriana dan C. succirubra dalam kultur in vitro Hairy root culture of Cinchona ledgeriana and C. succirubra by in vitro culture

2016 ◽  
Vol 72 (2) ◽  
Author(s):  
Nurita TORUAN-MATHIUS ◽  
. REFLINI ◽  
. NURHAIMI-HARIS ◽  
. JOKO-SANTOSO ◽  
A PRIANGANI-ROSWIEM
Keyword(s):  
Hairy Root ◽  
Hairy Roots ◽  
Basal Medium ◽  
Root Culture ◽  
Hairy Root Culture ◽  
Chain Reaction ◽  
Ri Plasmid ◽  
Polymerase Chain ◽  
Cinchona Ledgeriana

Summary Problems encountered in hairy root culture  of  C. ledgeriana and C. succirubra are low percentage of transformation of explants by Agrobacterium rhizogenes and slow growth of hairy root. The objective of this research was to evaluate the potential of several A. rhizogenes strains for initiation  hairy roots of  C. succirubra and C. ledgeriana, and to obtain the best medium for hairy root culture of Cinchona spesies. Axenic shoot and leaves explants of eight-month-old of C. ledgeriana and  C. succirubra seedlings were inoculated with A. rhizogenes strain ATCC-15834, ATCC-8196,    R-20001, 07-20001, A4, R-MAFFA, TISTR509, TISTR510 and LBA9457. Inoculated explants were cultured in solid MS medium with the addition of 100 mg/L amphicylin. Subculture of the hairy root was performed by transferred of root pieces into fresh liquid basal medium MS, B5, White and Heller. Hairy roots from the best of basal medium were subcultured on the same medium with the addition of 50  and 100 mg/L   L-tryptophane, three or five times concentration of MS vitamins. The integration of T-DNA of   A. rhizogenes in hairy root was confirmed with specific primer for TL and TR-DNA of plasmid by Polymerase Chain Reaction analysis. The results showed that only A. rhizogenes strain  LBA 9457 were effective for  transformation of explants from both Cinchona species. The fastest hairy roots growth were found  in MS medium, while growth in others medium was poor. Hairy roots of  C. ledgeriana has vigor and growth better than hairy roots of C. succirubra. MS with the addition of 50 mg/L  L-tryptophane and  three times the concen-trations of vitamin  is the best medium for hairy root growth and vigor. Hairy roots of  C. succirubra and C. ledgeriana used in this studies were confirmed that hairy roots  contained TL and TR-DNA region of Ri plasmid with molecular weight 780 and 1600 bp.  The results showed that strain of A. rhizogenes, plant species, source of explant and composition of medium affect the initiation, growth, development  and vigor of hairy roots.Ringkasan Masalah dalam kultur akar rambut  C. ledgeriana dan C. succirubra adalah rendahnya tingkat keberhasilan transformasi eksplan dengan Agrobacterium rhizogenesdan pertumbuhannya yang lambat. Penelitian ini bertujuan untuk mengevaluasi  potensi dari beberapa galur A. Rhizogenes untuk inisiasi, mendapatkan komposisi medium terbaik untuk pertumbuhan akar rambut C. ledgeriana dan C. succirubra, serta konfirmasi terintegrasinya TR dan TL-DNA Ri plasmid ke dalam jaringan eksplan.  Eksplan batang  dan  daun  berasal  dari kecambah aksenik C. ledgeriana dan C. succirubra berumur delapan bulan diinokulasi dengan A. rhizogenes galur 15834, 8196, R-20001, 07-20001, A4, R.MAFFA,TISTR 509, TISTR 510 dan LBA 9457. Eksplan yang sudah diinokulasi dikulturkan dalam medium MS padat. Subkultur dilakukan dengan cara mentransfer potongan ujung akar rambut ke dalam medium cair MS, B5, White dan Heller. Akar rambut dari medium kultur yang terbaik kemudian disubkultur ke dalam medium yang sama dengan penambahan 50 dan 100 mg/L L-triptofan dengan konsentrasi vitamin sebanyak tiga kali dan lima kali dari konsentrasi normal MS. Integrasi T-DNA dalam akar rambut dikonfirmasi meng-gunakan Polymerase Chain Reaction  dengan primer spesifik untuk TL dan TR-DNA plasmid. Hasil yang diperoleh menunjukkan bahwa hanya A.rhizogenes galur LB9457 yang efektif menginfeksi eksplan baik batang maupun daun dari kedua spesies kina. Induksi, pertumbuhan dan vigor akar rambut yang terbaik diperoleh dari medium MS dengan penambahan 50 mg/L L-triptofan dan tiga kali konsentrasi vitamin. Hasil konfirmasi akar rambut baik dari batang maupun daun menggunakan PCR, menunjukkan bahwa TL dan TR-DNA dari Ri plasmid  A. rhizogenes mampu menghasilkan pita-pita DNA dengan BM780 dan 1600 pb. Hasil yang diperoleh menunjukkan bahwa galur  A. rhizogenes, spesies tanaman, sumber eksplan dan komposisi medium berpengaruh terhadap inisiasi, pertumbuhan,  perkembangan dan vigor akar rambut.

scholarly journals The Presence of the Hairy-Root-Disease-Inducing (Ri) Plasmid in Wheat Endophytic Rhizobia Explains a Pathogen Reservoir Function of Healthy Resistant Plants

2020 ◽  
Vol 86 (17) ◽  
Author(s):  
Byoungwoo Kang ◽  
Taichi Maeshige ◽  
Aya Okamoto ◽  
Yui Kataoka ◽  
Shinji Yamamoto ◽  
...  
Keyword(s):  
Plant Species ◽  
Hairy Root ◽  
Crown Gall ◽  
Species Complex ◽  
Screening Method ◽  
High Ratio ◽  
Rhizobium Radiobacter ◽  
Content Type ◽  
Root Diseases ◽  
Ri Plasmid

ABSTRACT A large number of strains in the Rhizobium radiobacter species complex (biovar 1 Agrobacterium) have been known as causative pathogens for crown gall and hairy root diseases. Strains within this complex were also found as endophytes in many plant species with no symptoms. The aim of this study was to reveal the endophyte variation of this complex and how these endophytic strains differ from pathogenic strains. In this study, we devised a simple but effective screening method by exploiting the high resolution power of mass spectrometry. We screened endophyte isolates from young wheat and barley plants, which are resistant to the diseases, and identified seven isolates from wheat as members of the R. radiobacter species complex. Through further analyses, we assigned five strains to the genomovar (genomic group) G1 and two strains to G7 in R. radiobacter. Notably, these two genomovar groups harbor many known pathogenic strains. In fact, the two G7 endophyte strains showed pathogenicity on tobacco, as well as the virulence prerequisites, including a 200-kbp Ri plasmid. All five G1 strains possessed a 500-kbp plasmid, which is present in well-known crown gall pathogens. These data strongly suggest that healthy wheat plants are reservoirs for pathogenic strains of R. radiobacter. IMPORTANCE Crown gall and hairy root diseases exhibit very wide host-plant ranges that cover gymnosperm and dicot plants. The Rhizobium radiobacter species complex harbors causative agents of the two diseases. Recently, endophyte isolates from many plant species have been assigned to this species complex. We isolated seven endophyte strains belonging to the species complex from wheat plants and revealed their genomovar affiliations and plasmid profile. The significance of this study is the finding of the genomovar correlation between the endophytes and the known pathogens, the presence of a virulence ability in two of the seven endophyte strains, and the high ratio of the pathogenic strains in the endophyte strains. This study therefore provides convincing evidence that could unravel the mechanism that maintains pathogenic agents of this species and sporadically delivers them to susceptible plants.

scholarly journals Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Jose A. Valdes Franco ◽  
Ray Collier ◽  
Yi Wang ◽  
Naxin Huo ◽  
Yong Gu ◽  
...  
Keyword(s):  
Agrobacterium Rhizogenes ◽  
Genome Sequence ◽  
Hairy Root ◽  
Wild Type Strain ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Virulence Plasmid ◽  
Wild Type ◽  
Circular Chromosome ◽  
Transgenic Roots

This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic roots). Disarmed variants of the strain have been used to produce stable transgenic monocot and dicot plants.

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