Sequencing and Analysis of the Complete Mitochondrial Genome of Penicillium Citrinum in Hunan Yiyang Dark Tea

HU Zhiyuan; LIU Suchun; XU Zhenggang; LIU Shiquan; WEN Xin

doi:10.13305/j.cnki.jts.2020.06.010

Journal of Tea Science >

2020 , Vol. 40 >Issue 6: 830 - 844

DOI: https://doi.org/10.13305/j.cnki.jts.2020.06.010

Research Paper

Sequencing and Analysis of the Complete Mitochondrial Genome of Penicillium Citrinum in Hunan Yiyang Dark Tea

HU Zhiyuan ,
LIU Suchun ,
XU Zhenggang ,
LIU Shiquan ,
WEN Xin

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1. College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China;
2. School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China;
3. Hunan Institute of Food Quality Supervision Inspection and Research, Changsha 410111, China

Received date: 2020-01-16

Revised date: 2020-03-30

Online published: 2020-12-10

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Abstract

In this study, the mitochondrial genome sequence of a strain of Penicillium citrinum isolated from dark tea was determined and analyzed, and its phylogenetic relationship with the closely related microorganisms was explored. The result shows that the mitochondrial genome of Penicillium citrinum is a circular DNA molecule with a length of 27β537βbp, which encodes 42 genes. The genome bases are composed of A (36.17%), T (37.06%), C (11.82%) and G (14.95%). All the 15 protein-coding genes use typical ATG as the start codon, TAA or TAG as the stop codon. Its gene sequences are similar to those of the reported Penicillium species and are conserved in evolution. The highly occurred amino acids in the protein-coding genes are Leu, Ile, Ser and Phe. The top 4 codons with the high RSCU frequency are UUA, AUA, UUU and GGU, respectively. There are 30 G-U mismatches in 24 tRNA genes, all of which could form typical cloverleaf structure. Phylogenetic analysis shows that the most closely related taxonomic status of Penicillium citrinum is Penicillium ShG4C, followed by Penicillium polonicum and Penicillium nordicum.

Key words： dark tea; Penicillium citrinum; mitochondrial genome; phylogeny

Cite this article

HU Zhiyuan , LIU Suchun , XU Zhenggang , LIU Shiquan , WEN Xin . Sequencing and Analysis of the Complete Mitochondrial Genome of Penicillium Citrinum in Hunan Yiyang Dark Tea[J]. Journal of Tea Science, 2020 , 40(6) : 830 -844 . DOI: 10.13305/j.cnki.jts.2020.06.010

References

[1] Desmond E, Brochier-Armanet C, Forterre P, et al.On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes[J]. Research in Microbiology, 2011, 162(1): 53-70.
[2] Hua Y Q, Yan Z T, Fu W B, et al.Sequencing and analysis of the complete mitochondrial genome in Anopheles culicifacies (Diptera: Culicidae)[J]. Mitochondrial DNA Part A, 2015, 27(4): 2909-2910.
[3] Houbraken J A M P, Frisvad J C, Samson R A. Taxonomy of Penicillium citrinum and related species[J]. Fungal Diversity, 2010, 44(1): 117-133.
[4] Haas D, Pfeifer B, Reiterich C, et al.Identification and quantification of fungi and mycotoxins from Pu-erh tea[J]. International Journal of Food Microbiology, 2013, 166(2): 316-322.
[5] 粟清. 真菌单菌株固态发酵茶叶及其产Teadenol化合物分析[D]. 昆明: 云南大学, 2018.
Su Q.Fungal solid-state fermentation teas and its teadenol-producing potentiality [D]. Kunming: Yunnan University, 2018.
[6] 赵仁亮, 谭吉慧, 卢秦华, 等. 茯砖茶发花微生物生物学特性研究[J]. 茶叶科学, 2016, 36(2): 160-168.
Zhao R L, Tan J H, Lu Q H, et al.Biological characterization of fungi involved in fu brick tea fermentation[J]. Journal of Tea Science, 2016, 36(2): 160-168.
[7] 熊元元. 四川黑茶渥堆微生物多样性及空气微生物研究[D]. 雅安: 四川农业大学, 2017.
Xiong Y Y.Study on Microbial diversity of Sichuan dark tea during post-fermentation and airborne microbial [D]. Ya'an: Sichuan Agricultural University, 2017.
[8] 姜依何, 胥伟, 朱旗. 黑茶真菌污染研究进展及探讨[J]. 茶叶科学, 2018, 38(3): 227-236.
Jiang Y H, Xu W, Zhu Q.Research progress and discussion on fungal contamination of dark tea[J]. Journal of Tea Science, 2018, 38(3): 227-236.
[9] Li T T, Jiang G X, Qu H X, et al.Comparative transcriptome analysis of Penicillium citrinum cultured with different carbon sources identifies genes involved in citrinin biosynthesis[J]. Toxins, 2017, 9(2): 69. doi: 10.3390/toxins9020069.
[10] Föllmann W, Behm C, Degen G H.Toxicity of the mycotoxin citrinin and its metabolite dihydrocitrinone and of mixtures of citrinin and ochratoxin A in vitro[J]. Archives of Toxicology, 2014, 88(5): 1097-1107.
[11] 赵兴丽, 张金峰, 周玉锋, 等. 一株拮抗茶炭疽病菌的木霉菌的分离、筛选及鉴定[J]. 茶叶科学, 2019, 39(4): 431-439.
Zhao X L, Zhang J F, Zhou Y F, et al.Isolation, Screening and identification of a strain of trichoderma antagonizing tea anthracnose[J]. Journal of Tea Science, 2019, 39(4): 431-439.
[12] Wu L, Zhao Y L, Xu Z G, et al.The complete mitochondrial genome and phylogeny of Geospiza magnirostris (Passeriformes: Thraupidae)[J]. Conservation Genetics Resources, 2019, 11: 191-193.
[13] Patel R K, Mukesh J.NGS QC Toolkit: a toolkit for quality control of next generation sequencing data[J]. Plos One, 2012, 7(2): e30619. doi: 10.1371/journal.pone.0030619.
[14] Peng Y, Leung H C M, Yiu S M, et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth[J]. Bioinformatics, 2012, 28(11): 1420-1428.
[15] Donath A, Jühling F, Externbrink F, et al.MITOS: Improved de novo metazoan mitochondrial genome annotation[J]. Molecular Phylogenetics and Evolution, 2013, 69(2): 313-319.
[16] Lohse M, Drechsel O, Bock R.OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes[J]. Current Genetics, 2007, 52: 267-274.
[17] Lowe T M, Eddy S R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Research, 1997, 25(5): 955-964.
[18] Rasmus W.FeatureExtract-extraction of sequence annotation made easy[J]. Nucleic Acids Research, 2005, 33(s2): 567-569.
[19] Xia X H, Xie Z.DAMBE: software package for data analysis in molecular biology and evolution[J]. Journal of Heredity, 2001, 92(4): 371-373.
[20] 周思倩, 焦伟丽, 彭珠黎, 等. 埃博拉病毒基因组中微卫星序列的分布分析[J]. 基因组学与应用生物学, 2019, 38(3): 1087-1095.
Zhou S Q, Jiao W L, Peng Z L, et al.Analysis of microsatellite sequence distribution in Ebolavirus genomes[J]. Genomics and Applied Biology, 2019, 38(3): 1087-1095.
[21] 彭艳, 陈斌, 李廷景. 黄侧异腹胡蜂线粒体基因组全序列测定和分析[J]. 昆虫学报, 2017, 60(4): 464-474.
Peng Y, Chen B, Li T J.Sequencing and analysis of the complete mitochondrial genome of Parapolybia crocea (Hymenoptera: Vespidae)[J]. Acta Entomologica Sinica, 2017, 60(4): 464-474.
[22] 孔华忠. 中国真菌志(第三十五卷): 青霉属及其相关有性型属[M]. 北京: 科学出版社, 2007: 121-124.
Kong H Z.Mycolography of China(vol.35): Penicillium and its related sex type [M]. Beijing: Science Press, 2007: 121-124.
[23] Hu Z Y, Liu S Q, Xu Z G, et al.Complete mitochondrial genome and phylogenetic analysis of Penicillium citrinum in dark tea[J]. Mitochondrial DNA Part B, 2019, 4(2): 2445-2446.
[24] Joardar V, Abrams N F, Hostetler J, et al.Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability[J]. BMC Genomics, 2012, 13(1): 698. doi: 10.1186/1471-2164-13-698
[25] Eldarov M A, Mardanov A V, Beletsky A V, et al.Complete mitochondrial genome of compactin-producing fungus Penicillium solitum and comparative analysis of Trichocomaceae mitochondrial genomes[J]. FEMS Microbiology Letters, 2012, 329(1): 9-17.
[26] Mardanov A V, Glukhova L B, Gruzdev E V, et al.The complete mitochondrial genome of the acid-tolerant fungus Penicillium ShG4C[J]. Genomics Data, 2016, 10: 141-143.
[27] Sun X, Li H, Yu D.Complete mitochondrial genome sequence of the phytopathogenic fungus Penicillium digitatum and comparative analysis of closely related species[J]. Fems Microbiology Letters, 2011, 323(1): 29-34.
[28] Woo P, Zhen H, Cai J, et al.The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts[J]. Febs Letters, 2003, 555(3): 469-477.
[29] Ellegren H.Microsatellites: simple sequences with complex evolution[J]. Nature Reviews Genetics, 2004, 5(6): 435-445.
[30] Kang X, Liu C, Liu D, et al.The complete mitochondrial genome of huperzine A-producing endophytic fungus Penicillium polonicum[J]. Mitochondrial Dna Part B Resources, 2016, 1(1): 202-203.
[31] Avise J C.The history and purview of phylogeography: a personal reflection[J]. Molecular Ecology, 1998, 7(4): 371-379.
[32] 李宏俊, 张晶晶, 袁秀堂, 等. 利用线粒体COI和微卫星标记分析文蛤7个地理群体的遗传变异[J]. 生态学报, 2016, 36(2): 499-507.
Li H J, Zhang J J, Yuan X T, et al.Genetic diversity and differentiation of seven geographical populations of hard clam (Meretrix meretrix) assessed by COI and microsatellite markers[J]. Acta Ecologica Sinica, 2016, 36(2): 499-507.
[33] 连总强, 滚双宝, 李力, 等. 基于第二代测序技术兰州鲇线粒体基因组全序列测定与分析[J]. 水生生物学报, 2017, 41(2): 334-345.
Lian Z Q, Gun S B, Li L, et al.Sequencing and analysis of the complete mitochondrial genome of Silurus Lanzhouensis based on next generation sequencing technologies[J]. Acta Hydrobiologica Sinica, 2017, 41(2): 334-345.
[34] 刘小丽, 孙佼, 韩金巧, 等. 岛屿生境下黄毛鼠种群的遗传变异[J]. 生态学报, 2019, 39(18): 6898-6907.
Liu X L, Sun J, Han J Q, et al.Genetic variation of Rattus losea populations in island habitats[J]. Acta Ecologica Sinica, 2019, 39(18): 6898-6907.
[35] Morin P A, Archer F I, Foote A D, et al.Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species[J]. Genome Research, 2010, 20(7): 908-916.
[36] 赵振军, 童华荣, 周黎, 等. 普洱茶中真菌种群的分离与分子鉴定[J]. 茶叶科学, 2009, 29(6): 436-442.
Zhao Z J, Tong H R, Zhou L, et al.Isolation and molecular identification of fungal colonization of Pu-erh tea[J]. Journal of Tea Science, 2009, 29(6): 436-442.
[37] 刘石泉, 赵运林, 胡治远. DGGE法初步解析茯砖茶发花过程中真菌群落结构[J]. 生态学杂志, 2014, 33(10): 2687-2693.
Liu S Q, Zhao Y L, Hu Z Y.Analysis of fungal community structure during the Fahua-fermentation process of Fuzhuan Brick Tea by DGGE technology[J]. Chinese Journal of Ecology, 2014, 33(10): 2687-2693.
[38] Karaoglu S A, Ulker S.Isolation, identification and seasonal distribution of soilborne fungi in tea growing areas of Iyidere-Ikizdere vicinity (Rize-Turkey)[J]. Journal of Basic Microbiology, 2006, 46(3): 208-218.
[39] Weber C C, Hurst L D.Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster[J]. Journal of Molecular Evolution, 2010, 71(5-6): 415-426.
[40] Khalil A M A, Hashem A H, Abdelaziz A M. Occurrence of toxigenic Penicillium polonicum in retail green table olives from the Saudi Arabia market[J]. Biocatalysis and Agricultural Biotechnology, 2019, 21: 101314. doi: 10.1016/j.bcab.2019.101314
[41] Iacumin L, Manzano M, Andyanto D, et al.Biocontrol of ochratoxigenic moulds (Aspergillus ochraceus and Penicillium nordicum) by Debaryomyces hansenii and Saccharomycopsis fibuligera during speck production[J]. Food Microbiology, 2017, 62: 188-195.
[42] Visagie C M, Houbraken J, Frisvad J C, et al.Identification and nomenclature of the genus Penicillium[J]. Studies in Mycology, 2014, 78: 343-371.

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