Complete mitochondrial genome and phylogenetic analysis of  Penicillium citrinum  in dark tea

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Abstract

Penicillium citrinum is a common polluting microorganism in dark tea production. Our study was performed to report the complete mitochondrial genome of P. citrinum. The mitochondrial genome of P. citrinum was a circular DNA molecule of 27,537 bp in length, encoding 42 genes as follows: 15 PCGs, two rRNAs, 24 tRNAs, and an independent ORF. A (36.14%), T (37.06%), C (11.83%), and G (14.98%) was composed of genomic bases. In addition, phylogenetic analysis showed that Penicillium sp. exhibited a closest relationship with the taxonomic status of P. citrinum.

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MITOS: improved de novo metazoan mitochondrial genome annotation.

Matthias Bernt, Alexander Donath, Frank Jühling … (2013)

About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.

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NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

Ravi K. Patel, Mukesh Jain (2012)

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

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Toxicity of the mycotoxin citrinin and its metabolite dihydrocitrinone and of mixtures of citrinin and ochratoxin A in vitro.

Wolfram Follmann, G Degen, C Behm (2014)

Citrinin (CIT) and ochratoxin A (OTA) are mycotoxins produced by several species of the genera Aspergillus, Penicillium and Monascus. Both can be present as contaminants in various food commodities and in animal feed. The occurrence and toxicity of OTA and human exposure have been intensively studied, but for CIT such data are scarce by comparison. Recently, dihydrocitrinone (DH-CIT) was detected as main metabolite of CIT in human urine, and co-occurrence of CIT and OTA was shown in human blood plasma (Blaszkewicz et al. in Arch Toxicol 87:1087-1094, 2013). In light of these new findings, we have now investigated the toxicity of the metabolite DH-CIT in comparison with CIT and analysed the effects of mixtures of CIT and OTA in vitro. The cytotoxic potency of DH-CIT (IC50 of 320/200 μM) was distinctly lower compared with CIT (IC50 of 70/62 μM) after treatment of V79 cells for 24 and 48 h. Whereas CIT induced a concentration-dependent increase in micronucleus frequencies at concentrations ≥30 μM, DH-CIT showed no genotoxic effect up to 300 μM. Thus, conversion of CIT to DH-CIT in humans can be regarded as a detoxification step. Mixtures of CIT and OTA exerted additive effects in cytotoxicity assays. The effect of CIT and OTA mixtures on induction of micronuclei varied dependent on the used concentrations between additive for low μM concentrations and more-than-additive for high μM concentrations. Effects on cell cycle were mostly triggered by OTA when both mycotoxins were used in combination. The implications of our and related in vitro studies are discussed with respect to in vivo concentrations of CIT and OTA, which are found in animals and in humans.

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Journal ID (nlm-ta): Mitochondrial DNA B Resour

Journal ID (iso-abbrev): Mitochondrial DNA B Resour

Title: Mitochondrial DNA. Part B, Resources

Publisher: Taylor & Francis

ISSN (Electronic): 2380-2359

Publication date (Electronic, pub): 12 July 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 2445-2446

Affiliations

[a ]College of Food Science and Technology, Hunan Agricultural University , Changsha, China;

[b ]Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University , Yiyang, China

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CONTACT Suchun Liu huzhiyuan2019@ 123456163.com College of Food Science and Technology, Hunan Agricultural University , Changsha410128, China

Article

Publisher ID: 1637794

DOI: 10.1080/23802359.2019.1637794

PMC ID: 7687588

SO-VID: 3fdba3f1-d444-4277-9b3f-87502d17063c

License:

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 use, distribution, and reproduction in any medium, provided the original work is properly cited.

Complete mitochondrial genome and phylogenetic analysis of Penicillium citrinum in dark tea

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Arabidopsis genomics

Most cited references 9

MITOS: improved de novo metazoan mitochondrial genome annotation.

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

Toxicity of the mycotoxin citrinin and its metabolite dihydrocitrinone and of mixtures of citrinin and ochratoxin A in vitro.

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