A Genome-Sequence Survey for Ascogregarina taiwanensis Supports Evolutionary Affiliation but Metabolic Diversity between a Gregarine and Cryptosporidium

ABSTRACT Candida parapsilosis is responsible for ca. 15% of Candida infections and is of particular concern in neonates and surgical intensive care patients. The related species Candida albicans has recently been shown to possess a functional mating pathway. To analyze the analogous pathway in C. parapsilosis, we carried out a genome sequence survey of the type strain. We identified ca. 3,900 genes, with an average amino acid identity of 59% with C. albicans. Of these, 23 are predicted to be predominantly involved in mating. We identified a genomic locus homologous to the MTL a mating type locus of C. albicans, but the C. parapsilosis type strain has at least two internal stop codons in the MTL a 1 open reading frame, and two predicted introns are not spliced. These stop codons were present in MTL a 1 of all eight C. parapsilosis isolates tested. Furthermore, we found that all isolates of C. parapsilosis tested appear to contain only the MTL a idiomorph at the presumptive mating locus, unlike C. albicans and C. dubliniensis. MTLα sequences are present but at a different chromosomal location. It is therefore likely that all (or at least the majority) of C. parapsilosis isolates have a mating pathway that is either defective or substantially different from that of C. albicans.

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A genome sequence survey of the mollicute corn stunt spiroplasmaSpiroplasma kunkelii

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2002.tb11153.x ◽

2002 ◽

Vol 210 (1) ◽

pp. 7-17 ◽

Cited By ~ 19

Author(s):

Xiaodong Bai ◽

Saskia A Hogenhout

Keyword(s):

Genome Sequence ◽

Corn Stunt ◽

Genome Sequence Survey ◽

A Genome

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Faculty Opinions recommendation of Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.737748193.793574951 ◽

2020 ◽

Author(s):

Zhaosheng Kong

Keyword(s):

Gossypium Hirsutum ◽

Genome Evolution ◽

Genome Sequence ◽

Gossypium Arboreum ◽

A Genome ◽

Gossypium Herbaceum

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Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

Nucleic Acids Research ◽

10.1093/nar/gkaa1134 ◽

2020 ◽

Vol 48 (22) ◽

pp. 12604-12617

Author(s):

Pengpeng Long ◽

Lu Zhang ◽

Bin Huang ◽

Quan Chen ◽

Haiyan Liu

Keyword(s):

Genome Sequence ◽

Energy Function ◽

Structural Information ◽

Structural Data ◽

P Values ◽

A Genome ◽

Z Scores ◽

Transcription Regulators ◽

Dna Specificity ◽

Tetracycline Repressor

Abstract We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.

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Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽

10.3390/genes12020246 ◽

2021 ◽

Vol 12 (2) ◽

pp. 246

Author(s):

Xiaomeng Chen ◽

Rui Li ◽

Yonglin Wang ◽

Aining Li

Keyword(s):

Genome Sequence ◽

Extracellular Enzymes ◽

De Novo ◽

Whole Genome Sequence ◽

Hybrid Poplars ◽

A Genome ◽

Conserved Genes ◽

Genomic Characterization ◽

Molecular Bases ◽

Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

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Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain ∆6

Genome Announcements ◽

10.1128/genomea.00759-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 3

Author(s):

Daniel R. Reuß ◽

Andrea Thürmer ◽

Rolf Daniel ◽

Wim J. Quax ◽

Jörg Stülke

Keyword(s):

Bacillus Subtilis ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Full Genome Sequence ◽

Subtilis Strain ◽

Full Genome ◽

Biotechnological Applications ◽

A Genome ◽

Subtilis Subsp

Bacillus subtilis ∆6 is a genome-reduced strain that was cured from six prophages and AT-rich islands. This strain is of great interest for biotechnological applications. Here, we announce the full-genome sequence of this strain. Interestingly, the conjugative element ICE Bs 1 has most likely undergone self-excision in B. subtilis ∆6.

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Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1

Genome Announcements ◽

10.1128/genomea.01367-17 ◽

2018 ◽

Vol 6 (4) ◽

Cited By ~ 3

Author(s):

Peng Sun ◽

Haifeng Luo ◽

Xin Zhang ◽

Jingyi Xu ◽

Yanan Guo ◽

...

Keyword(s):

Genome Sequence ◽

Single Molecule ◽

Whole Genome Sequence ◽

Mycoplasma Bovis ◽

Sequencing Technology ◽

Circular Chromosome ◽

A Genome ◽

Variable Surface ◽

Integrative Conjugative Elements ◽

Single Circular Chromosome

ABSTRACT A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.

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The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

Wellcome Open Research ◽

10.12688/wellcomeopenres.17204.1 ◽

2021 ◽

Vol 6 ◽

pp. 258

Author(s):

Konrad Lohse ◽

Alexander Mackintosh ◽

Roger Vila ◽

◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Sex Chromosome ◽

Gene Annotation ◽

Protein Coding ◽

Individual Male ◽

Protein Coding Genes ◽

A Genome ◽

Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

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The genome sequence of the common malachite beetle, Malachius bipustulatus (Linnaeus, 1758)

Wellcome Open Research ◽

10.12688/wellcomeopenres.17381.1 ◽

2021 ◽

Vol 6 ◽

pp. 322

Author(s):

Liam Crowley ◽

◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Sex Chromosome ◽

Individual Female ◽

A Genome ◽

The Common

We present a genome assembly from an individual female Malachius bipustulatus (the common malachite beetle; Arthropoda; Insecta; Coleoptera; Melyridae). The genome sequence is 544 megabases in span. The majority (99.70%) of the assembly is scaffolded into 10 chromosomal pseudomolecules, with the X sex chromosome assembled.

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