Phylo-taxonogenomics supports revision of taxonomic status of twenty Xanthomonas pathovars to Xanthomonas citri

2021 ◽  
Author(s):  
Kanika Bansal ◽  
Sanjeet Kumar ◽  
Prabhu B. Patil
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Published Data ◽  
Xanthomonas Citri ◽  
Genome Sequence Data ◽  
Major Species

Based on phylo-taxonogenomics criteria, we present amended descriptions for twenty pathovars to Xanthomonas citri. Incidentally, eighteen were first reported from India. Seven out of twenty are currently classified as X. axonopodis, twelve out of twenty as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining sixteen were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. The present proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants.

scholarly journals Taxonomic repositioning of twelve Xanthomonas campestris, seven Xanthomonas axonopodis and one Pseudomonas cissicola reference pathovars to Xanthomonas citri

2021 ◽  
Author(s):  
Kanika Bansal ◽  
Sanjeet Kumar ◽  
Prabhu B Patil
Keyword(s):  
Genome Sequence ◽  
Xanthomonas Campestris ◽  
Sequence Data ◽  
Published Data ◽  
Xanthomonas Citri ◽  
Xanthomonas Axonopodis ◽  
Genome Sequence Data ◽  
Taxonomic Confusion

Here on the basis of phylo-taxonogenomics criteria we present amended description of 20 pathovars to Xanthomonas citri majority (18/20) of which were first reported from India. 7/20 are currently classified as X. axonopodis, 12/20 as X. campestris and 1/20 as Pseudomonas cissicola. Here, we have generated genome sequence data for 4 pathovars and genomes of remaining 16 were used from the published data. Genome based investigation reveals that all these pathovars belong to X. citri and not to X. axonopodis or X. campestris as previously reported. Present proposal is to aid in resolving the taxonomic confusion of the X. ctiri pathovars and prevent future usage of invalid names.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Data in Brief ◽  
2021 ◽  
Vol 35 ◽  
pp. 106784
Author(s):  
Chinda Chhe ◽  
Ayaka Uke ◽  
Sirilak Baramee ◽  
Umbhorn Ungkulpasvich ◽  
Chakrit Tachaapaikoon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Paenibacillus Sp

scholarly journals Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽  
2020 ◽  
Vol 33 ◽  
pp. 106416
Author(s):  
Asset Daniyarov ◽  
Askhat Molkenov ◽  
Saule Rakhimova ◽  
Ainur Akhmetova ◽  
Zhannur Nurkina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lynsey K. Whitacre ◽  
Jesse L. Hoff ◽  
Robert D. Schnabel ◽  
Sara Albarella ◽  
Francesca Ciotola ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Birth Defect ◽  
Genetic Basis ◽  
Sequence Data ◽  
Model Organism ◽  
Bubalus Bubalis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Draft genome sequence data of a chromium reducing bacterium, Bacillus licheniformis strain KNP

Data in Brief ◽  
2021 ◽  
Vol 34 ◽  
pp. 106640
Author(s):  
Pankaj Kumar Arora ◽  
Rupali Mishra ◽  
Rishabh Anand Omar ◽  
Raj Shekhar Saroj ◽  
Alok Srivastava ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bacillus Licheniformis ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Genome Sequence Data ◽  
Bacterium Bacillus
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