Nucleic Acids Research, 2020 1
doi: 10.1093/nar/gkaa957

Wenyu Shi1,2,† , Qinglan Sun1,2,3,† , Guomei Fan1,2 , Sugawara Hideaki4 , Ohkuma Moriya5 ,Takashi Itoh5 , Yuguang Zhou6 , Man Cai6 , Song-Gun Kim7 , Jung-Sook Lee7 , Ivo Sedlacek8 ,David R. Arahal9 , Teresa Lucena9 , Hiroko Kawasaki10 , Lyudmila Evtushenko11 ,Bevan S. Weir 12 , Sarah Alexander13 , Dlauchy Dénes14 , Somboon Tanasupawat15 ,Lily Eurwilaichitr3,16 , Supawadee Ingsriswang3,16 , Bruno Gomez-Gil17 ,Manzour H. Hazbón18 , Marco A. Riojas18 , Chatrudee Suwannachart19 , Su Yao20 ,Peter Vandamme21 , Fang Peng22 , Zenghui Chen1,2 , Dongmei Liu1,2 , Xiuqiang Sun1,2 ,Xinjiao Zhang1,2 , Yuanchun Zhou23 , Zhen Meng23 , Linhuan Wu 1,2,24,* and Juncai Ma1,2,3,24,*
1

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101,
China, 2 World Data Center for Microorganisms, Beijing 100101, China, 3 China-Thailand Joint Laboratory on
Microbial Biotechnology, Beijing 100190, China, 4 National Institute of Genetics, Yata, Mishima 411-8540, Japan,
5Japan Collection of Microorganisms (JCM)/ Microbe Divion, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba,
Ibaraki 305-0074, Japan, 6 China General Microbiological Culture Collection Center (CGMCC), Institute ofMicrobiology, Chinese Academy of Sciences, Beijing 100101, China, 7 Korean Collection for Type Cultures (KCTC),
Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212,
Republic of Korea, 8 Czech Collection of Microorganisms, Masaryk University, Kamenice 5, building A25, 625 00
Brno, Czech Republic, 9 Colección Española de Cultivos Tipo (CECT), and Departamento de Microbiologı́a yEcologı́a, University of Valencia, 46100 Burjassot (Valencia), Spain, 10 NITE Biological Resource Center (NBRC),
National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan,
11
All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology ofMicroorganisms RAS, Pushchino, Moscow region 142290, Russia, 12 Mycology & Bacteriology Systematics, Manaaki
Whenua – Landcare Research, Auckland, New Zealand, 13 National Collection of Type Cultures (NCTC), Public
Health England (PHE), UK, 14 National Collection of Agricultural and Industrial Microorganisms, Faculty of Food
Science, Szent István University, H-1118, Budapest, Somlói út 14-16, Hungary, 15 Faculty of Pharmaceutical
Sciences, Chulalongkorn University (PCU), Bangkok 10330, Thailand, 16 Thailand Bioresource Research Center(TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology
Development Agency (NSTDA), Thailand, 17 CIAD, A.C., Collection of Aquatic Important Microorganisms (CAIM). AP
711 Mazatlán, Sinaloa, Mexico, 18 American Type Culture Collection(ATCC), 10801 University Boulevard, Manassas,
VA 20110, USA, 19 Biodiversity Research Centre, Thailand Institute of Scientific and Technological Research (TISTR),
35 M 3 Technopolis Khlong 5 Khlong Luang Pathum Thani 12120, Thailand, 20 China Center of Industrial Culture
Collection (CICC), Beijing, China, 21 BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences,Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium, 22 China Center for Type Culture Collection(CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China, 23 Computer Network Information
Center, Chinese Academy of Sciences, Beijing 100190, China and 24 State Key Laboratory of Microbial Resources,
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
Received August 11, 2020; Revised October 06, 2020; Editorial Decision October 07, 2020; Accepted October 28, 2020

* To whom correspondence should be addressed. Tel: +86 10 64807385; Fax: +86 10 64807426; Email: wulh@im.ac.cn

Correspondence may also be addressed to Juncai Ma. Tel: +86 10 64807422; Fax: +86 10 64807426; Email: ma@im.ac.cn†

The authors wish it to be known that the first two authors should be regarded as joint first authors.

C The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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gcType: a high-quality type strain genome databasefor microbial phylogenetic and functional research2 Nucleic Acids Research, 2020

ABSTRACTINTRODUCTION
Microorganisms are considered the most abundant organisms in the world. It is estimated that ∼4–6 × 1030 prokaryotic cells exist on Earth, comprising a biomass of 350–550
× 1015 g of carbon (1). The total number of prokaryotic
species is up to 109 (2). Approximately 1800 bacterial andarchaeal species names were published in approved lists ofbacterial names in 1980 (3). Thereafter, names published inoriginal articles or in the ‘Validation Lists’ of the International Journal of Systematic and Evolutionary Microbiology(IJSEM) have been validated. As of September 2020, thisnumber increased to 16 763.
The description of a prokaryotic species needs to designate its type strain, whose phenotypes and genotypes areoften well characterised and described. 16S rRNA gene
and whole-genome sequences derived from type strains, together with phenotypic and chemotaxonomic characteristics are used for taxonomic identification. Thus, type strainsare critical references for the characterisation of species andthe identification of isolates and strains for taxonomic purposes (4). Currently, the type strains from the 16 763 listed
species are available as 67 331 catalogue numbers from over
130 culture collections.
For several decades, it has been recognised that the complete deoxyribonucleic acid (DNA) sequence of a species
would be the standard reference to determine their phy-

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Taxonomic and functional research of microorganisms has increasingly relied upon genome-based
data and methods. As the depository of the Global
Catalogue of Microorganisms (GCM) 10K prokaryotic
type strain sequencing project, Global Catalogue ofType Strain (gcType) has published 1049 type strain
genomes sequenced by the GCM 10K project which
are preserved in global culture collections with avalid published status. Additionally, the information
provided through gcType includes >12 000 publicly
available type strain genome sequences from GenBank incorporated using quality control criteria andstandard data annotation pipelines to form a highquality reference database. This database integrates
type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches andinteractive interfaces have allowed extensive exploration of the database’s resources. In this study, we
describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which
could serve as a one-stop platform for the identification of prokaryotic species. The number of typestrain genomes that are published will continue toincrease as the GCM 10K project increases its collaboration with culture collections worldwide. Dataof this project is shared with the International Nucleotide Sequence Database Collaboration. Accessto gcType is free at http://gctype.wdcm.org/.

logeny, which in turn determines their taxonomic classification (5). With the increasing availability of genome sequences, genome-based methods such as average aminoacid identity, average nucleotide identity (ANI) and digital
DNA–DNA hybridization (dDDH) have been developed asimportant measurements for prokaryotic taxonomy (6–8).
Since January 2018, IJSEM requires authors of new taxa
to provide genome sequences with descriptions of the noveltaxa for their manuscripts to be eligible for publication.
Data on 16S rRNA similarity, overall genome similarity or
distance and phenotypic and physiological information areused in combination to identify a new species (9).
Another essential element of microbial taxonomy is thecorrect assessment of phylogenetic relationships via the reconstruction of phylogenetic trees. Although phenotypic,
chemotaxonomic and genotypic information are useful for
identifying microorganisms, such information is often insufficient for reconstructing accurate phylogenies. The increasing availability of microbial genome sequences allows
for more comprehensive and accurate depictions of phylogenetic relationships to study the origin and evolution ofprokaryotic organisms.
Because of their genomic and hence metabolic and functional diversity, microorganisms serve as ideal models forbiotechnology studies. Combined with comprehensive phenotypic and physiological information, genome sequencesof type strains enable the connection of genes with functions and provide insights into the metabolic and functional
potential of microorganisms. Therefore, accruing data on
genomes of microorganisms will greatly promote biotechnology studies.
Given the immense efforts of microbiologists and community sequencing projects such as The Genomic Encyclopedia of Bacteria and Archaea (GEBA) (10), thenumber of publicly available genome sequences of typestrains continues to increase rapidly. Currently, there are>12 000 genome sequences in the International Nucleotide
Sequence Database Collaboration (INSDC). However, alarge number of microbial type strains remain to be sequenced. Therefore, the World Data Centre for Microorganisms (WDCM) GCM 10K project (11) is cooperatingwith culture collections across the world to fill the current gap in whole-genome databases for validly publishedspecies as well as with IJSEM to provide free sequencing and genome annotation services for newly described
species (12).
With increasing microbial genomic information, thedatabases and servers which host and analyse thesedata continue to expand. The Genomes Online Database(GOLD) (13) in conjunction with the Integrated Microbial Genomes (IMG) (14) provide a comprehensive catalogue of microbial genomes and platform for the analysisof microbial genomes and microbiomes. The Type (Strain)
Genome Server (15), which is connected to the comprehensive prokaryotic metadata resources BacDive (16) and
LPSN (17), is considered a high-throughput web server for
genome-based prokaryotic taxonomy. However, there is stilla need for a database that provides not only up-to-date typestrains and the associated comprehensive genome information but also user-friendly searchable and comparable functions.

Nucleic Acids Research, 2020 3

DATABASE DESIGN AND IMPLEMENTATION
gcType portal and search functions
Users of the platform can query the database and performgenomic analyses using the gcType portal. gcType is the
GCM 10K sequencing project data portal for the dissemination of information and publication of updated sequencing results. It currently provides multiple, flexible searchfunctions for users to explore its resources (Figure 1). A
text-based advanced search option allows users to conduct
cross-genome searches through a single or combination of
metadata information. The input query retrieves all datacontaining the corresponding keywords in the metadatafields, such as the sequencing status, library or contig or
scaffold numbers.
All validly published species have been mapped onto the
National Center for Biotechnology Information (NCBI)
taxonomy ID (18), and all genome sequences have been
mapped onto the Genome Taxonomy Database (GTDB)
system using GTDB-Tk (19). Users can browse throughthese taxonomic trees to search for sequenced and unsequenced species. Sequence-based searches against pregenerated type strain 16S rRNA sequence databases using the Basic Local Alignment Search Tool (BLAST) areprovided as well. The resultant hits of the query sequences
are displayed as alignments and links to the matched typestrains.
A statistics page displaying tables with genomic characteristics provides gcType users with an overview of the diversity of microbial genomic data. In particular, these tables
feature the guanine-cytosine (GC) content, average genome
size, number of predicted genes and functional annotation
results among different phyla. Interactive interfaces allow
users to further explore the features of various taxonomic
groups.
Integrated information for type strains
Comprehensive taxonomic, phenotypic, physiological andgenomic information is organised by type strain species(Figure 2A-2D). The taxonomic status, 16S rRNA genesequence and NCBI taxonomy ID are provided. One orseveral ‘genome sequence project’ pages are linked withthe type strain page. For genome sequences extracted frompublic resources, GenBank (20) or GOLD ‘Bioproject’,‘Biosample’ and ‘Assembly IDs’ are provided as links to theoriginal sites in GenBank. Simultaneously, a ‘GCM project
number’ is assigned to the sequence and linked to the annotation results generated by the GCM microbial genomic
annotation pipeline. Metadata from the genome sequences(e.g. library, N50 and GC content) as well as annotation results of the genome are listed by hits from various reference
databases such as COG (21), KEGG (22) and CARD (23).
Finally, It also incorporates open-source web applications:
JBrowse (24), a linear genome viewer, and CGView (25), a
circular genome viewer.
Data sourcesType strain information. Lists of validly published species,
a list of type strains, a list of type strains by culture collection, and a comprehensive list of 16S rRNA gene andgenome sequences are provided. New prokaryotic taxa wereconsidered validly published only if their names were published in the International Journal of Systematic Bacteriology (until October 1999) or the renamed IJSEM (from January 2000 to present). Names published in an original article, or the ‘Validation Lists’ are considered to be valid (26).
The list of species with validly published names were manually collected from IJSEM novel species articles and the validation lists. All data were collected until September 2020.
IJSEM and the International Committee on Systematics ofProkaryotes require the type strains of new taxa to be deposited in at least two recognised culture collections in two
countries. The deposition of type strains and related metadata information has been described in IJSEM articles. For
candidate type strains of novel species, taxonomists who request free genome sequencing services from WDCM are
asked to provide detailed metadata of the type strains before WDCM formally accepts their proposal. The metadatafields are following the description recommended by theminimum information about a genome sequence (MIGS)
specification (27).
16S rRNA gene sequence data. 16S rRNA gene sequences
similarity comparison remains the initial step in the identification of prokaryotic species workflow; therefore, a highquality 16S rRNA gene sequence database of species withvalidly published names is fundamental for conducting taxonomy studies. Some reference databases for 16S rRNA
gene sequences, e.g. EzBiocloud (28), SILVA (29) and RDP(30), provide online resources based on different data integration strategies and filtering criteria (31). Because gcType is designed for type strain-based taxonomic studies,
we collected 16S rRNA gene sequences from two sources.
The first contains 16S rRNA gene sequences from publicly
available resources, including 16S rRNA genes or sequences
derived from completed or partial genomes by RNAmmer(32). Their accession numbers were obtained from GenBank, and the associated sequence data were then extracted.
Second, for the GCM 10K sequencing project, prior to proceeding with whole-genome sequencing, submitted strainsare validated via 16S rRNA sequencing. The sequences
obtained from the GCM 10K project were added to the
database to allow the quality of type strains to be examined

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To facilitate access to and maximise the value of genome
sequences of type strains, the GCM 10K type strain sequencing project developed the gcType platform. This platform integrates publicly available information from otherdatabases along with the sequencing efforts of GCM 10K
project according to strict quality control standards, followed by a powerful standard data-processing pipeline toyield a high-quality reference database that provides webbased data analysis pipelines for genomic analysis andgenome-based species identification. Moreover, it associatestaxonomic, phenotypic and physiological information withthe type strains to enable users to conduct comprehensive
genomic and functional analyses. On the whole, gcType isa unique and useful resource that permits microbial taxonomists and microbiologists to gather up-to-date information on microbial type strain sequences.

4 Nucleic Acids Research, 2020

because a small percentage the strains are incorrect, likely
due to deposition or preservation errors. Data were further
filtered and evaluated based on quality control criteria suchas sequence length, number of ambiguous bases, completeness and the accuracy of the metadata. After alignment
with sequences in infernal (33) and Rfam (34) databases
and trimming of the 5 and 3 ends the two sources of 16SrRNA gene sequences were integrated to construct a reference dataset for the new species identification pipeline. Evaluation scores related to data quality are displayed on the
webpage and can be selected by users. Data processing is
described in Figure 3.
Genome sequencing information and sequence data. gcType publishes genome sequences and their annotation results from the GCM 10K sequencing project, which utilises
the next-generation sequencing (NGS) platform. To improve the quality of these sequences, we employ thirdgeneration sequencing (TGS) technologies (we are currently
using Pacific Biosciences) as a complementary, allowing forthe generation of completed or nearly completed bacterial genomes. Importantly, this combination strategy using
second- and third-generation sequencing platforms is used
for genome sequences that have been poorly assembled in
the second-generation sequencing platform alone (>50 contigs).
Raw sequence data that pass strict quality control criteria are run through the GCM microbial genome annotation
pipeline. Annotated sequences are then added to the gcType
type strain genome database.

Besides the genome sequences in the GCM 10K project,publicly available genome sequence data are extracted from
GenBank via their unique type strain numbers. Genome sequences with gene prediction results provided by GenBankin FASTA format were used to perform a GCM microbial genome annotation pipeline; genome sequences without gene prediction results were used to perform a genomic
component analysis followed by annotation using the GCM
microbial genome annotation pipeline. These newly annotated type strain sequences are then incorporated into thegcType Type strain genome database.
To create a non-redundant set of representative genomes,
genome sequences are further filtered by the number ofcontigs, genome sizes and N50 statistics. Sequences withnumber of contigs larger than 500 are filtered in the reference database. A single, high-quality representative sequence from each species is selected to create the reference
dataset for the new species identification pipeline. Scores
pertaining to the quality of the genome are displayed on
the webpage and can be selected if there is more than one
sequence. A schematic representation of data processing isshown in Figure 3.
As of September 2020, gcType contains 13 962 prokaryotic type strain genomes, from which 1049 were producedby the GCM 10K sequencing project.
Database design
gcType uses the open-source MySQL relational databasemanagement system to manage the data. This database con-

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Figure 1. Features of the gcType portal: a map of the main pages and list of the subordinate pages on the gcType website.

Nucleic Acids Research, 2020 5

tains tables that are continuously updated with information on species’ taxonomy and nomenclature. Phenotypicand physiological metadata descriptions are linked withproper taxa status. The sequencing projects and their associated metadata and annotation results are linked to thetype strains. Scaffolds and predicted features from genomic
analyses are related to the assembled genome.
gcType follows an identifier system similar to that of
INSDC, in which a ‘GCM Biosample’ number is assigned
to each type strain and a ‘GCM Bioproject’ number toeach sequencing project. For type strains that have beensequenced multiple times and thus have several sets of sequencing results, different ‘GCM Bioproject’ numbers are
assigned to each sequencing effort, a ‘locus tag’ is assigned
to each predicted gene and an ‘assembly number’ is assigned
to the assembled genome.

DATA ANALYSIS PIPELINES
Currently, owing to difficulties in using multiple bioinformatics tools and programming scripts for in-house analyses,
taxonomists often rely on commercial sequencing and data
analysis services to generate genome sequences. However,
due to a wide range of data models, annotation pipelines
and versions of reference databases, the results of analysing
the same genome vary greatly. Functional assignments generated from the same gene using different resources may
generate very different results (35).
High-quality valid databases that include the 16S rRNA
gene and genome sequences are prerequisites for taxonomic
classification and identification. Because these pipelines aredesigned for taxonomic purposes, only data of type strains
with validly published names are included. Therefore, gc-

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Figure 2. Comprehensive information about a type strain and its associated genome sequences. (A) Species information and marker genes. The NCBI
taxonomy ID is linked to the NCBI taxonomy database. (B) Project and sequencing information. (C) Genome annotation results with the associatedstatistics. (D) Interactive circular view of type strain genome.

6 Nucleic Acids Research, 2020

A

B

Figure 4. Workflow of gcType data analysis pipelines. (A) GCM microbial genome assembly and annotation pipeline. (B) New species identification
pipeline.

Type features two reference database integrated pipelines:
genome assembly and annotation pipeline and the new
species identification pipeline.
Genome assembly and annotation pipeline
The genome assembly and annotation pipeline comprises
three analytical procedures (Figure 4A): (i) processing of
raw reads and assembly, (ii) genomic component analysis
and (iii) gene annotation.

(1) Processing of raw reads and assemblyA) If TGS long reads (PacBio or Nanopore reads) areprovided as the input, the raw sequencing reads aretrimmed and assembled into contigs or scaffolds using
Canu (36) or Flye (37). If NGS short reads (Illumina
paired-end reads) are also provided, they will be used
to enhance contigs or scaffolds using Pilon (38).
B) If only NGS short reads are provided, raw reads aretrimmed into clean reads using Sickle (https://github.
com/najoshi/sickle) or Trimmomatic (39), corrected us-

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Figure 3. Schematic representation of gcType for data processing: Two sources of 16S rRNA gene sequences are integrated to form the gcType 16S rRNA
gene database. Sequence data is further aligned and trimmed to form a reference database for a new species identification pipeline. Publicly available genome
sequences and GCM 10K genome sequences are processed by the GCM microbial genome annotation pipeline to form a type strain genome database.
The assembled genomes from these two sources are integrated after quality control to form a type strain genome reference database for a new species
identification pipeline.

Nucleic Acids Research, 2020 7

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Figure 5. Submission pages and results of the analysis for the two pipelines, provided by gcType. (A) Submission page of a genome assembly and annotation
pipeline. Different analytical tools and annotation databases are provided. (B) Submission page of a species identification pipeline. (C) Pages of the online
results include parameters selected by the user, logs, report and output file. (D) An example of a phylogenetic analysis based on marker genes from a species
identification pipeline.

8 Nucleic Acids Research, 2020

New species identification pipeline
For the new species identification pipeline (shown in Figure 4B), the new type strain genome sequence is used as thequery in a similarity search against the gcType 16S rRNA
gene and genome sequence reference database following therecommendations for the use of genome data in IJSEM.
First, 16S rRNA gene sequence(s) are extracted fromthe submitted query genome sequence. If a full-length 16S
rRNA sequence of the same type strain sequenced using
the Sanger method is available, it is compared with the 16S
rRNA sequence extracted from the whole-genome assembly
to ensure authenticity of the data.
Second, the 16S rRNA gene sequence is aligned to the gcType 16S rRNA gene database using the BLAST tool. Sequences with the highest similarity are used to estimate 16S
rRNA gene completeness (58). Users are allowed to selecta set of 16S rRNA gene sequences for further phylogenetic
analyses from neighbouring sequences or sequences with aremote distance to serve as the reference.
Third, the submitted genome sequence is aligned to thegcType whole-genome reference database using Mash (59)to calculate the genome distance. Various genome similarity metrics, including ANIb (60), FastANI (61), orthoANIb
and orthoANIu (62), are provided for the calculation ofsimilarity between a submitted genome sequence and theselected sequences.
Finally, selected 16S rRNA gene sequences are aligned
using MAFFT (63) or MUSCLE (64). Then, MEGA (65),
FastTree (66) and RAxML (67) are used to perform phylogenetic analyses. For the selected genome sequences, 56
marker genes (68) are extracted and used to perform phylogenetic analyses.
Online services and results of analyses of these twopipelines are displayed in Figure 5A-5D.

Table 1. Top 10 culture collections with the largest number of type strains
No.

Culturecollection

Country

Preserved typestrainsa

Sequenced typestrains

1
2
3
4
5
6
7
8
9
10

DSMZ
JCM
ATCC
BCCM/LMG
NBRC
KCTC
CCUG
CIP
NRRL
CGMCC

GermanyJapan
United States
BelgiumJapan
Korea
SwedenFranceUnited States
China

9106
7200
4477
3513
3369
3243
3030
2784
1592
1558

3963
824
911
385
716
220
176
61
606
145

a The number of type strains preserved in each culture collection was man-ually extracted from IJSEM. Type strains which were obtained from otherculture collections by exchange of strains were not included.

RESULTS AND DISCUSSION
The ability to accurately identify and organise microorganisms into appropriate taxonomic groups is essential
for the functional research of microorganisms. With considerable advancements in genome sequencing and data
analytics, genomics is the most powerful and efficientmethod for studying the origins, evolution and interactions of a species and the diversity of the microbial world.
As the taxonomic representatives of various species, typestrains are very essential resources for genome sequencing. Currently, type strains are preserved in internationally renowned culture collections such as Leibniz-Institut
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Japan Collection of Microorganisms (JCM)/RIKEN BioResource Center and American
Type Culture Collection. The number of type strains andthe diversity of species are increasing in culture collections across the world. The top five culture collections withthe largest type strain deposition account for 88.02% of
all validly published species, and 97.13% of all publishedspecies are represented in ten culture collections.
The operations of microbial collections have changed
enormously over the past 20 years owing to the availability of multidisciplinary data as well as advances in analytical methods and bioinformatics. Traditional culture collections have made great efforts to explore the diversity of microorganisms and collect information on their genes, properties and products. For instance, with the joint effort of
the Department of Energy (DOE) Joint Genome Institute(JGI) (69), DSMZ has already published 3,963 type strain
genome sequences (Table 1). Large lists of published strain
sequences are limited to culture collections that allocate
large budgets to sequence, analyse and publish these sequences. Because this is not feasible for most collections,
the GCM 10K project can assist them in getting their items
sequenced and published while still being available for theirrepositories.
The number of sequenced bacterial and archaeal
genomes has grown exponentially in recent years. As
a sequencing center, DOE JGI is currently the largest
generator of type strain sequences and has published3066 sequences to date, followed by WDCM, which has

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ing Musket (40) and independently assembled into contigs or scaffolds using multiple assemblers (e.g. SOAPdenovo2 (41), SPAdes (42), Velvet (43) and Platanus(44)). Then, the best assembly result is selected according to N50, N75, the contig number, the length of thelargest contig and the number of total bases and ambiguous bases. Thereafter, the reads are mapped to thebest assembly result to check for mis-assemblies andevaluate the reads coverage.
C) The final assembly result (i.e. best assembly) is used
to estimate the completeness and contamination of the
genome using checkM (45) and to perform further genomic component analysis.
(2) Genomic component analysis: Genomic component
analysis involves CRISPR array recognition using
PILER-CR (46), repetitive structure detection using
TRF (47), non-coding RNA prediction using tRNAscanSE (48) and RNAmmer and gene prediction using Prodigal (49). The analysis is performed based on
the final assembly result.
(3) Gene annotation: Predicted genes are annotated using
several databases, including KEGG, GO (50), COG,
NR (51), Swiss-Prot (52), AntiSMASH (53), MetaCyc(54), PHI (55), Pfam (56), CARD and VFDB (57).

Nucleic Acids Research, 2020 9

Table 2. Sequencing efforts of global sequencing centres
Sequencing centres

1
2
3
4
5
6
7
8
9
10

DOE Joint Genome Institute (JGI)
WDCM GCM 10K project
National Institute of Technology and Evaluation
University of Tokyo
Shanghai Majorbio Bio-pharm Technology Co.
J. Craig Venter InstituteBroad InstituteWashington University in St. Louis
Wellcome Trust Sanger Institute
Baylor College of Medicine
Others

3066
1049
386
272
183
147
131
125
97
95
7784

Figure 6. Current sequencing status of prokaryotic organisms by different orders. Top five phyla with the largest number of orders are highlighted. Publishedtype strain genomes of the GCM 10K project are widely distributed in various orders. For orders that have more than nine species (nine is the median
number of species of all orders), the order names are coloured in grey if <50% of species have type strain genome sequences, indicating more sequencing
efforts should be focussed on these orders.

published 1049 genome sequences of type strains after twoyear of working with the GCM 10K sequencing project.
The data collected in the GCM 10K project is the resultof a collaboration of 22 global culture collections. The
National Institute of Technology and Evaluation and the
University of Tokyo rank third and fourth, generating
386 and 272 type strain genome sequences, respectively,
with most of these strains coming from the Biological
Resource Center/National Institute of Technology and
Evaluation (NBRC) and JCM. The top ten sequencing
centres contribute 42% of the total number of sequences,while the remaining 58% is contributed by 477 sequencing
centres (Table 2).
To date, whole-genome sequences of >13 962 type strains
are publicly available. However, over one-fourth of all bacterial type strains have yet to be sequenced (Figure 6). Amongthe sequenced type strains, less than 21% (2,911) have highquality, completed genomes. The remaining 11 051 genomes
have been published as draft genomes, meaning that each
one is composed of numerous contigs or scaffolds rather
than a single contiguous and complete sequence. These
draft sequences are valuable for some applications but do

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Number of publicly available typestrain genomesNo.

10 Nucleic Acids Research, 2020

FUTURE DIRECTIONS
Although taxonomic and phylogenetic analyses based on
16S rRNA gene sequences are commonly used methods
for bacterial identification, the prevalence of genome-basedtaxonomy has become more prevalent as a result of the increasing availability of high-quality reference databases anduser-friendly analysis pipelines. Taxonomists are required toprovide ANI or dDDH comparisons to type strains whenidentifying isolates, proposing new species, or reclassifying accepted species. However, because many type strain
genomes of species with validly published names remain unsequenced, taxonomists require these additional type strain
genomes so that their target strains can be analysed with appropriate scientific rigour. To address this critical need, theGCM 10K project is providing free sequencing services tocomplete these efforts, which are now complemented by thegcType platform.
In the future, gcType will continuously integrate datafrom various resources and publish updated results of the
GCM 10K type strain sequencing project, making it aunique resource for comprehensive type strain genome information. gcType will also integrate data pertaining to
genomic and phenotypic characteristics of a taxonomic
group to help define associations between genomic and phenotypic characteristics and further predict metabolic features based on the combination of the integrated information. Finally, as the high-quality reference genomic data
will provide accurate taxonomic and functional predictions
for metagenomic data, genome assemblies from metagenomic samples will be integrated to expand the utility ofthe database for uncultured prokaryotic organisms.
DATA AVAILABILITY
There are no access restrictions for the academic use of theplatform. All public available genomic data or metadata
are freely accessible. Both the 16S rRNA gene sequences
and whole-genome sequences generated by the GCM 10K
project have been continuously submitted to INSDC after data curation. Access to gcType is free at: http://gctype.
wdcm.org/.
ACKNOWLEDGEMENTS
We would like to thank the members of the World Federation for Culture Collections for the GCM 10K sequencing
project. We would like to thank the supports from National
Institute of Genetics (NIG) members, Professor Yasukazu
Nakamura, Dr Yasuhiro Tanizawa and Asami Fukuda for
their helps on data curation and annotation. We would also
like to thank the technical support staff at BGI Shenzhen
for their sequencing services and Ronglian for the cloudbased computing platform.

FUNDING
National Key Research Program of China [2017YFD0400302, 2017YFC1201202, 2018YFD0400201]; International Partnership Program of the Chinese Academyof Sciences [153211KYSB, 201900211]; Strategic Priority Research Program of the Chinese Academy of Sciences [XDA19050301]; 13th Five-year Informatization
Plan of the Chinese Academy of Sciences [XXH13506,
XXH13505]; Key Research Program of the Chinese
Academy of Sciences [KFZD-SW-219]; National Science
Foundation for Young Scientists of China [31701157,
31801106]; European Union and co-financed by European Social Fund [EFOP-3.6.3-VEKOP-16-2017-00005].
Funding for open access charge: International Partnership
Program of Chinese Academy of Sciences [153211KYSB
201900211].
Conflict of interest statement. None declared.

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