Draft Genome Sequence of  Daldinia childiae  JS-1345, an Endophytic Fungus Isolated from Stem Tissue of Korean Fir

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Abstract

The fungus Daldinia childiae strain JS-1345, isolated from stem tissue of Abies koreana (Korean fir), has shown strong anti-inflammatory activity. Here, we report the genome sequence of D. childiae JS-1345. The final assembly consisted of 133 scaffolds totaling 38,652,569 bp (G+C content, 44.07%).

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SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

Marten Boetzer, Walter Pirovano (2014)

Background The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data. Results Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes. Conclusions The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.

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FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.

Seryun Kim, Kyongyong Jung, Kyohun Ahn … (2008)

Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31,832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species. All data described in this study can be browsed through the FTFD web site at http://ftfd.snu.ac.kr/.

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HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

Shengfeng Huang, Zelin Chen, Guangrui Huang … (2012)

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus ( Branchiostoma belcheri ) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.

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Contributors

Jason E. Stajich: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (hwp): ga

Journal ID (pmc): mra

Journal ID (publisher-id): MRA

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic): 2 April 2020

Publication date Collection: April 2020

Volume: 9

Issue: 14

Electronic Location Identifier: e01284-19

Affiliations

[a ]Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea

[b ]Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, Center for Fungal Pathogenesis, Seoul National University, Seoul, South Korea

[c ]Department of Plant Medicine, Sunchon National University, Suncheon, South Korea

University of California, Riverside

Author notes

Address correspondence to Soonok Kim, sokim90@ 123456korea.kr .

Jung A Kim, Jongbum Jeon, and Sook-Young Park contributed equally to this work. Author order was determined in order of increasing seniority.

Citation Kim JA, Jeon J, Park S-Y, Jeon MJ, Yeo J-H, Lee Y-H, Kim S. 2020. Draft genome sequence of Daldinia childiae JS-1345, an endophytic fungus isolated from stem tissue of Korean fir. Microbiol Resour Announc 9:e01284-19. https://doi.org/10.1128/MRA.01284-19.

Article

Publisher ID: MRA01284-19

DOI: 10.1128/MRA.01284-19

PMC ID: 7118187

PubMed ID: 32241861

SO-VID: e3c8ef39-71d0-4055-a074-5dfa075cedaf

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 12 October 2019

Date accepted : 14 November 2019

Page count

Figures: 0, Tables: 0, Equations: 0, References: 22, Pages: 3, Words: 1861

Funding

Funded by: Ministry of Environment (MOE), https://doi.org/10.13039/501100003562;

Award ID: NIBR201830101

Award ID: NIBR201921101

Award Recipient : Soonok Kim

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cover-date April 2020

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Draft Genome Sequence of Daldinia childiae JS-1345, an Endophytic Fungus Isolated from Stem Tissue of Korean Fir

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Genome Integrity

Most cited references 15

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

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