scholarly journals Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition

2005 ◽  
Vol 187 (18) ◽  
pp. 6488-6498 ◽  
Author(s):  
Vinita Joardar ◽  
Magdalen Lindeberg ◽  
Robert W. Jackson ◽  
Jeremy Selengut ◽  
Robert Dodson ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Circular Chromosome ◽  
Physiological Level ◽  
Halo Blight ◽  
Bacterial Plant Pathogen ◽  
Reciprocal Best Hit ◽  
Reading Frames

ABSTRACT Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

scholarly journals The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Claudia B. Monteiro-Vitorello ◽  
Luis E. A. Camargo ◽  
Marie A. Van Sluys ◽  
João P. Kitajima ◽  
Daniela Truffi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Free Sugars ◽  
Sugar Transporters ◽  
Living Organisms ◽  
Bacterial Plant Pathogen ◽  
Single Circular Chromosome ◽  
Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

scholarly journals Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX2351 Isolated from Asian Citrus Psyllids in Texas, USA

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Madhurababu Kunta ◽  
Zheng Zheng ◽  
Fengnian Wu ◽  
John V. da Graca ◽  
Jong-Won Park ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
South Texas ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Rna Genes ◽  
Reading Frames

ABSTRACT We report here the draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351, collected from Asian citrus psyllids in south Texas, USA. The TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted open reading frames, and 52 RNA genes.

scholarly journals Complete Genome Sequence of Riemerella anatipestifer Serotype 10 Strain HXb2

2017 ◽  
Vol 5 (18) ◽  
Author(s):  
Qinghai Hu ◽  
Jingjing Qi ◽  
Huimin Bo ◽  
Guangqing Liu ◽  
Minjie Tao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Content Type ◽  
Riemerella Anatipestifer ◽  
Single Circular Chromosome ◽  
Reading Frames

ABSTRACT The complete genome sequence of highly virulent Riemerella anatipestifer strain HXb2 was determined. The genome consisted of a single circular chromosome of 2,425,237 bp containing 2,383 putative open reading frames (ORFs), 9 rRNA operons, and 40 tRNA genes.

scholarly journals Whole-Genome Sequence of “ Candidatus Profftella armatura” from Diaphorina citri in Guangdong, China

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
F. Wu ◽  
X. Deng ◽  
G. Liang ◽  
J. Huang ◽  
Y. Cen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Diaphorina Citri ◽  
Reading Frames

The genome of “ Candidatus Profftella armatura” strain YCPA from Diaphorina citri in Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp, 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs.

scholarly journals Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX1712 from Citrus in Texas

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
W. Cai ◽  
Z. Yan ◽  
J. Rascoe ◽  
M. J. Stulberg
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Candidatus Liberibacter Asiaticus ◽  
Content Type ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Reading Frames

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX1712, obtained from a Texas citrus tree, is reported here. Strain TX1712 has a draft genome size of 1,203,333 bp, a G+C content of 36.4%, 1,230 predicted open reading frames, and 41 RNAs and comprises 97.4% of the psy62 reference genome.

scholarly journals Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Rina Shinjo ◽  
Kazuma Uesaka ◽  
Kunio Ihara ◽  
Kseniia Loshakova ◽  
Yuri Mizuno ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Reading Frames

The complete genome sequence of the endophytic diazotroph Kosakonia sacchari , isolated from a sweet potato, was analyzed. The 4,902,106-bp genome with 53.7% G+C content comprises 4,638 open reading frames, including nif genes, 84 tRNAs, and seven complete rRNAs in a circular chromosome.

scholarly journals De Novo Whole-Genome Sequence of Xylella fastidiosa subsp. multiplex Strain BB01 Isolated from a Blueberry in Georgia, USA

2017 ◽  
Vol 5 (6) ◽  
Author(s):  
Christopher Van Horn ◽  
Chung-Jan Chang ◽  
Jianchi Chen
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Rna Genes ◽  
Reading Frames

ABSTRACT This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%, 2,943 open reading frames (ORFs), and 48 RNA genes.

scholarly journals Complete Genome Sequence of Flavobacterium psychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis

2017 ◽  
Vol 5 (8) ◽  
Author(s):  
Tatiana Rochat ◽  
Paul Barbier ◽  
Pierre Nicolas ◽  
Valentin Loux ◽  
David Pérez-Pascual ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Coho Salmon ◽  
Oncorhynchus Kisutch ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Reading Frames

ABSTRACT We report here the complete annotated genome sequence of Flavobacterium psychrophilum OSU THCO2-90, isolated from Coho salmon (Oncorhynchus kisutch) in Oregon. The genome consists of a circular chromosome with 2,343 predicted open reading frames. This strain has proved to be a valuable tool for functional genomics.

scholarly journals Whole-Genome Sequence of Oryctes rhinoceros Nudivirus from Riau Province, Indonesia

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Yudistira Wahyu Kurnia ◽  
Zulfikar Achmad Tanjung ◽  
Condro Utomo ◽  
Mohammad Naim ◽  
Elizabeth Caroline Situmorang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Dna Virus ◽  
Content Type ◽  
Oryctes Rhinoceros ◽  
Double Stranded Dna ◽  
The Family ◽  
Total Dna ◽  
Reading Frames

A double-stranded DNA virus, Oryctes rhinoceros nudivirus (OrNV), was detected in the total DNA of diseased larvae of O. rhinoceros in Riau Province, Indonesia. The complete genome sequence was 124,926 bp long and encodes 123 open reading frames (ORFs). This strain belongs to the family Nudiviridae and was designated LiboV.

scholarly journals Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria monocytogenes

2006 ◽  
Vol 188 (21) ◽  
pp. 7405-7415 ◽  
Author(s):  
Torsten Hain ◽  
Christiane Steinweg ◽  
Carsten Tobias Kuenne ◽  
André Billion ◽  
Rohit Ghai ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Listeria Innocua ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Circular Chromosome ◽  
Evolutionary Paths ◽  
Listeria Welshimeri

ABSTRACT We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an FoF1 ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of “fitness” genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.

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