Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

Download Full-text

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

Systematic Biology ◽

10.1093/sysbio/syv045 ◽

2015 ◽

Vol 64 (6) ◽

pp. 1000-1017 ◽

Cited By ~ 62

Author(s):

Alexander Nater ◽

Reto Burri ◽

Takeshi Kawakami ◽

Linnéa Smeds ◽

Hans Ellegren

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Related Species ◽

Whole Genome Sequencing Data ◽

Evolutionary Relationships ◽

Whole Genome ◽

Sequencing Data ◽

Closely Related Species

Download Full-text

Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype

Genome Announcements ◽

10.1128/genomea.01324-17 ◽

2017 ◽

Vol 5 (49) ◽

Cited By ~ 3

Author(s):

Taylor W. Bailey ◽

Naila C. do Nascimento ◽

Arun K. Bhunia

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Illumina Sequencing ◽

Foodborne Pathogen ◽

Whole Genome ◽

Content Type ◽

Serotype 1 ◽

Serotype 4B

ABSTRACT Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we performed whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b) using Illumina sequencing. The sequence showed 94.5% identity with strain F2365, serotype 4b, and 90.6% with EGD-e, serotype 1/2a.

Download Full-text

Whole-Genome Sequencing of Sphingobium sp. Strain RSMS, a Highly Efficient Tributyl Phosphate-Degrading Bacterium

Microbiology Resource Announcements ◽

10.1128/mra.00600-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Shyam Sunder Rangu ◽

Ashish Beck ◽

Mohak Sharda ◽

Rita Mukhopadhyaya ◽

Aswin Sai Narain Seshasayee ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Tributyl Phosphate ◽

Organic Pollutant ◽

Whole Genome ◽

Future Studies ◽

Genetic Elements ◽

Highly Efficient ◽

Degrading Bacterium

ABSTRACT Sphingobium sp. strain RSMS was described earlier as an efficient degrader of tributyl phosphate, an organic pollutant. This report describes the generation and annotation of the genome sequence of Sphingobium sp. strain RSMS, which will facilitate future studies to identify genetic elements responsible for the degradation of tributyl phosphate.

Download Full-text

Draft Genome Sequence of a Mycobacterium porcinum Strain Isolated from a Pet Cat with Atypical Mycobacterial Panniculitis

Microbiology Resource Announcements ◽

10.1128/mra.00006-20 ◽

2020 ◽

Vol 9 (11) ◽

Author(s):

Anthony Mannion ◽

Tina McCollester ◽

Alexander Sheh ◽

Zeli Shen ◽

Hilda Holcombe ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Fast Growing

A fast-growing Mycobacterium species was cultured from draining, purulent lesions on the caudal abdomen of a 12-year-old male domestic long-haired cat. Whole-genome sequencing identified the organism as Mycobacterium porcinum.

Download Full-text

Genome Sequence ofListeria monocytogenesStrain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994

Genome Announcements ◽

10.1128/genomea.00760-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 1

Author(s):

Arthur W. Pightling ◽

Hugh Rand ◽

Errol Strain ◽

Franco Pagotto

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Real Time ◽

Genome Sequencing ◽

Genome Sequence ◽

Foodborne Pathogen ◽

Environmental Isolate ◽

Severe Illness ◽

Whole Genome ◽

Serotype 1

Listeria monocytogenesis a foodborne pathogen that causes severe illness. Thus, ongoing efforts at real-time whole-genome sequencing are of utmost importance. However, it is also important that retrospective analyses that place these data into context be performed. Here, we present the genome sequence of strain HPB2088, which was collected in 1994.

Download Full-text

Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3

Genome Announcements ◽

10.1128/genomea.01275-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 5

Author(s):

Jennifer K. Bender ◽

Stefan Fiedler ◽

Ingo Klare ◽

Guido Werner

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Enterococcus Faecium ◽

Complete Genome ◽

Laboratory Strain ◽

Whole Genome ◽

Coding Sequences

The genome sequence of the commensal and widely used laboratory strain Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding sequences as assigned by NCBI.

Download Full-text

Complete Chloroplast Genome Sequence of Cane Needle Grass, Nassella hyalina (Poaceae: Stipeae)

Genome Announcements ◽

10.1128/genomea.01215-17 ◽

2017 ◽

Vol 5 (47) ◽

Author(s):

Aisuo Wang ◽

Hanwen Wu ◽

David Gopurenko

Keyword(s):

Whole Genome Sequencing ◽

Chloroplast Genome ◽

Genome Sequencing ◽

Genome Sequence ◽

Gene Content ◽

Whole Genome ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

Chloroplast Genome Sequence

ABSTRACT Nassella hyalina (cane needle grass) is on the Alert List for Environmental Weeds in Australia. We present here the first complete chloroplast sequence of N. hyalina reconstructed from Illumina whole-genome sequencing. The complete chloroplast sequence is 137,606 bp in size and has a gene content and structure similar to those of other published chloroplast genomes of Stipeae.

Download Full-text

Five-year Microevolution of a Multidrug-Resistant Mycobacterium Tuberculosis Strain within a Patient with Inadequate Compliance to Treatment.

10.21203/rs.3.rs-251738/v1 ◽

2021 ◽

Author(s):

Dario Fernández Do Porto ◽

Johana Monteserin ◽

Josefina Campos ◽

Ezequiel J Sosa ◽

Mario Matteo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Treatment Compliance ◽

Whole Genome Sequence ◽

Intermittent Therapy ◽

Whole Genome ◽

Short Term ◽

Depth Analysis

Abstract BackgroundWhole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported.Case Presentations In this work, we applied whole genome sequencing for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium. tuberculosis isolates obtained from a patient within 57-month of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patience, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy.ConclusionsThis report highlights the relevance of whole-genome sequencing in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

Download Full-text

Whole-genome sequencing reveals progressive versus stable myeloma precursor conditions as two distinct entities

Nature Communications ◽

10.1038/s41467-021-22140-0 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Bénedith Oben ◽

Guy Froyen ◽

Kylee H. Maclachlan ◽

Daniel Leongamornlert ◽

Federico Abascal ◽

...

Keyword(s):

Multiple Myeloma ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Monoclonal Gammopathy ◽

Whole Genome Sequence ◽

Whole Genome ◽

Driver Genes ◽

Smoldering Myeloma ◽

Undetermined Significance

AbstractMultiple myeloma (MM) is consistently preceded by precursor conditions recognized clinically as monoclonal gammopathy of undetermined significance (MGUS) or smoldering myeloma (SMM). We interrogate the whole genome sequence (WGS) profile of 18 MGUS and compare them with those from 14 SMMs and 80 MMs. We show that cases with a non-progressing, clinically stable myeloma precursor condition (n = 15) are characterized by later initiation in the patient’s life and by the absence of myeloma defining genomic events including: chromothripsis, templated insertions, mutations in driver genes, aneuploidy, and canonical APOBEC mutational activity. This data provides evidence that WGS can be used to recognize two biologically and clinically distinct myeloma precursor entities that are either progressive or stable.

Download Full-text

Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment

BMC Infectious Diseases ◽

10.1186/s12879-021-06069-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Darío A. Fernandez Do Porto ◽

Johana Monteserin ◽

Josefina Campos ◽

Ezequiel J. Sosa ◽

Mario Matteo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Intermittent Therapy ◽

Whole Genome ◽

Sequencing Analysis ◽

Short Term ◽

Depth Analysis

Abstract Background Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. Case presentation In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5′ untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. Conclusions This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

Download Full-text