Evidence map›Paper›PMID 25678942›Full record

ArticleStandards in genomic sciences2015

Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.

Xiao-Yang Gao, Xiao-Yang Zhi, Hong-Wei Li, Yu Zhou, Alla Lapidus, James Han, Matthew Haynes, Elizabeth Lobos, Marcel Huntemann, Amrita Pati and 8 more

Open access · goldAbstract read
In one paragraph

Article in Standards in genomic sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
7.4field-weighted citation impact, top 2% 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

4 citing papers in PubMed, 98 citations in OpenAlex.

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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

18 authors at 8 institutions in 5 countries.

Xiao-Yang GaoKey Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China ; University of Chinese Academy of Sciences, Beijing, China.
Xiao-Yang ZhiKey Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
Hong-Wei LiKey Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China ; The First Hospital of Qujing City, Qujing Affiliated Hospital of Kunming Medical University, Qujing, China.
Yu ZhouState Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest Control, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
Alla LapidusTheodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
James HanDOE Joint Genome Institute, Walnut Creek, California, USA.
Matthew HaynesDOE Joint Genome Institute, Walnut Creek, California, USA.
Elizabeth LobosDOE Joint Genome Institute, Walnut Creek, California, USA.
Marcel HuntemannDOE Joint Genome Institute, Walnut Creek, California, USA.
Amrita PatiDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia N IvanovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos MavromatisDOE Joint Genome Institute, Walnut Creek, California, USA.
Brian J TindallLeibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Victor MarkowitzBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Tanja WoykeDOE Joint Genome Institute, Walnut Creek, California, USA.
Hans-Peter KlenkLeibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany ; School of Biology, Newcastle University, Newcastle upon Tyne, UK.
Nikos C KyrpidesDOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Wen-Jun LiKey Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China ; Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
Joint Genome Institute · USYunnan University · CNLeibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · DEChinese Academy of Sciences · CNKing Abdulaziz University · SALawrence Berkeley National Laboratory · USSt Petersburg University · RUZheJiang Academy of Agricultural Sciences · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125(T) was isolated from a hypersaline lake in China. The genome of strain YIM 91125(T) becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125(T), together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125(T) with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.

Indexed as

AerobicChemoorganotrophicGram-negativeHalomonas luteaLake EbinurModerately halophilic

Identifiers

PMID25678942
PMCPMC4315136
OpenAlexW2131356304

What OpenQuestion holds

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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.