Evidence map›Paper›PMID 15317790›Full record

ArticleJournal of bacteriology2004

Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.

Michael P McLeod, Xiang Qin, Sandor E Karpathy, Jason Gioia, Sarah K Highlander, George E Fox, Thomas Z McNeill, Huaiyang Jiang, Donna Muzny, Leni S Jacob and 12 more

Open access · greenAbstract readComparative Study
In one paragraph

Article in Journal of bacteriology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
104citing papers in PubMed, 2 pooled it
16.8field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

104 citing papers in PubMed, 2 syntheses or guidelines pooled it, 239 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Adaptation ofmSphere · 2026
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  8. Metabolism and physiology of pathogenic bacterial obligate intracellular parasites.Frontiers in cellular and infection microbiology · 2024
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  15. Why is manganese so valuable to bacterial pathogens?Frontiers in cellular and infection microbiology · 2023
    Review
  16. Review
  17. Infection and immunity · 2022
    Review
  18. Genetic typing of isolates of Rickettsia typhi.PLoS neglected tropical diseases · 2022
    Article
  19. Prevalence and Molecular Characterization ofTropical medicine and infectious disease · 2021
    Article
  20. Article

44 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors at 4 institutions in 1 country.

Michael P McLeodHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030-7783, USA.
Xiang Qin
Sandor E Karpathy
Jason Gioia
Sarah K Highlander
George E Fox
Thomas Z McNeill
Huaiyang Jiang
Donna Muzny
Leni S Jacob
Alicia C Hawes
Erica Sodergren
Rachel Gill
Jennifer Hume
Maggie Morgan
Guangwei Fan
Anita G Amin
Richard A Gibbs
Chao Hong
Xue-Jie Yu
David H Walker
George M Weinstock
The University of Texas Health Science Center at Houston · USThe University of Texas Medical Branch at Galveston · USBaylor College of Medicine · USUniversity of Houston · US

Funding

TRAINING PROGRAM IN COMPUTATIONAL BIOLOGY AND MEDICINET15LM007093 · NLM · RICE UNIVERSITY · PI Lydia E. Kavraki · 1992 to 2026
$20.8M
COMPLETE GENOME SEQUENCE OF RICKETTSIA TYPHIU01AI049040 · NIAID · UNIVERSITY OF TEXAS MEDICAL BR GALVESTON · PI WALKER, DAVID H · 2000 to 2001
$368k
Multicopy Gene Families in Eukaryotic GenomesF33HG002551 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI FOX, GEORGE · 2002 to 2002
$54k
NHGRI NIH HHS F33-HG02551NIAID NIH HHS AI49040NLM NIH HHS LM07093NLM NIH HHS T15 LM007093
6 · The paper itself

Abstract

Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii. We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi, 15 are found only in R. conorii and R. typhi, and 24 are unique to R. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi, compared to R. prowazekii and R. conorii. In addition, we found a 124-kb R. typhi-specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii. Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii, which appears to have occurred after the typhus (R. prowazekii and R. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.

Indexed as

Genome, BacterialSequence Analysis, DNAChromosome InversionDNA, BacterialElectron Transport Complex IVFrameshifting, RibosomalGene Expression Regulation, BacterialGene RearrangementGenes, BacterialGenes, rRNAGenomicsMolecular Sequence DataPseudogenesRickettsiaRickettsia conoriiRickettsia typhiDNA, BacterialElectron Transport Complex IVRNA, TransferRNA, Untranslated

Identifiers

PMID15317790
PMCPMC516817
OpenAlexW2153232310

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.