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SeSaMe:Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms

Genomics, Proteomics & Bioinformatics 2020年第5期18卷 601-612页

作者： Jee Eun Kang antonio ciampi Mohamed Hijri Institut de Recherche en Biologie Vegetale Departement de Sciences BiologiquesUniversite de MontrealMontrealQC H1X 2B2Canada Department of Epidemiology Biostatistics and Occupational HealthMcGill UniversityMontrealQC H3A 1A2Canada Creative Research Initiatives Center for Molecular Biology of Translation School of Life SciencesKorea UniversitySeoul 02841Republic of Korea African Genome Center Agro BioSciencesMohammed Ⅵ Polytechnic University(UM6P)43150 Ben GuerirMorocco

Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia,resulting in a metagenome when whole-genome sequencing(WGS)data are obtained from sequencing AMF cultivated in vivo.The metagenome contains not only the AMF sequences,but also those from associated microorganisms.In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(SeSaMe),designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing.A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure.The program distinguishes between coding sequence(CDS)and non-CDS,and classifies a query sequence into a genus group out of 54 genera used as reference.The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at ***.

关键词： SeSaMe Spore-associated symbiotic microbes Arbuscular mycorrhizal fungi Taxonomic classification 3-codon DNA 9-mer

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SeSaMe PS Function:Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 613-623页

作者： Jee Eun Kang antonio ciampi Mohamed Hijri Institut de Recherche en Biologie Vegetale Departement de Sciences BiologiquesUniversite de MontrealQC H1X 2B2Canada Department of Epidemiology Biostatistics and Occupational HealthMcGill UniversityMontrealQC H3A 1A2Canada Creative Research Initiatives Center for Molecular Biology of Translation School of Life SciencesKorea UniversitySeoul 02841Republic of Korea African Genome Center AgroBioSciencesMohammed Ⅳ Polytechnic University(UM6P)43150 Ben GuerirMorocco

In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at ***.

关键词： SeSaMe Spore-associated symbiotic microbes Position-specific function Outlier Metagenome

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A systematic review and meta-analysis to determine the effect of sperm DNA damage on in vitro fertilization and intracytoplasmic sperm injection outcome

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Asian Journal of Andrology 2017年第1期19卷 80-90页

作者： Luke Simon Armand Zini Alina Dyachenko antonio ciampi Douglas T Carrell Department of Surgery (Urology) University of Utah School of Medicine Salt Lake City UT USA Division of Urology Department of Surgery St. Mary's Hospital Center St. Mary's Hospital 3830 Lacombe Avenue Montreal Quebec H3T 1M5 Canada Department of Human Genetics University of Utah School of Medicine Salt Lake City UT USA Department of Obstetrics and Gynecology University of Utah School of Medicine Salt Lake City UT USA.

Sperm DNA damage is prevalent among infertile men and is known to influence natural reproduction. However, the impact of sperm DNA damage on assisted reproduction outcomes remains controversial. Here, we conducted a meta-analysis of studies on sperm DNA damage （assessed by SCSA, TUNEL, SCD, or Comet assay） and clinical pregnancy after IVF and/or ICSI treatment from MEDLINE, EMBASE, and PUBMED database searches for this analysis. We identified 41 articles （with a total of 56 studies） including 16 IVF studies, 24 ICSI studies, and 16 mixed （IVF ＋ ICSI） studies. These studies measured DNA damage （by one of four assays： 23 SCSA, 18 TUNEL, 8 SCD, and 7 Comet） and included a total of 8068 treatment cycles （3734 IVF, 2282 ICSI, and 2052 mixed IVF ＋ ICSI）. The combined OR of 1.68 （95% Ch 1.49-1.89; P 〈 0.0001） indicates that sperm DNA damage affects clinical pregnancy following IVF and/or ICSI treatment. In addition, the combined OR estimates of IVF （16 estimates, OR = 1.65; 95% CI： 1.34-2.04; P 〈 0.0001）, ICSI （24 estimates, OR = 1.31; 95% Ch 1.08-1.59; P = 0.0068）, and mixed IVF ＋ ICSI studies （16 estimates, OR = 2.37; 95% Ch 1.89-2.97; P〈 0.0001） were also statistically significant. There is sufficient evidence in the existing literature suggesting that sperm DNA damage has a negative effect on clinical pregnancy following IVF and/or ICSI treatment.

关键词： assisted reproductive technology outcomes clinical pregnancy meta-analysis sperm DNA damage systematic review

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