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Investigation of the genetic etiology in male infertility with apparently balanced chromosomal structural rearrangements by genome sequencing

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Asian Journal of Andrology 2022年第3期24卷 248-254页

作者： Matthew Hoi Kin Chau Ying Li Peng Dai Mengmeng Shi Xiaofan Zhu Jacqueline Pui Wah Chung Yvonne K Kwok Kwong Wai Choy Xiangdong Kong Zirui Dong Department of Obstetrics and Gynaecology The Chinese University of Hong KongHong KongChina Shenzhen Research Institute The Chinese University of Hong KongShenzhen 518057China Hong Kong Hub of Paediatric Excellence The Chinese University of Hong KongHong KongChina Genetics and Prenatal Diagnosis Center The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics Hong KongChina

Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.

关键词： azoospermia balanced structural rearrangements genome sequencing male infertility severe oligospermia

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genome sequencing provides potential strategies for drug discovery and synthesis

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Acupuncture and Herbal Medicine 2023年第4期3卷 244-255页

作者： Chunsheng Zhao Ziwei Zhang Linlin Sun Ronglu Bai Lizhi Wang Shilin Chen School of Chinese Materia Medica Tianjin University of Traditional Chinese MedicineTianjinChina School of Chinese Materia Medica Chengdu University of Traditional Chinese MedicineChengduChina

Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.

关键词： Biosynthetic pathways Gene editing genome sequencing Medicinal plants Secondary metabolites

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Safety evaluation and whole genome sequencing for revealing the ability of Penicillium oxalicum WX-209 to safely and effectively degrade citrus segments

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Food Science and Human Wellness 2023年第6期12卷 2369-2380页

作者： Xiao Hu Yujiao Qian Zhipeng Gao Gaoyang Li Fuhua Fu Jiajing Guo Yang Shan Hunan Agriculture Product Processing Institute International Joint Lab on Fruits&Vegetables ProcessingQuality and SafetyHunan Key Lab of Fruits&Vegetables StorageProcessingQuality and SafetyHunan Academy of Agricultural SciencesChangsha 410125China College of Animal Science and Technology Hunan Agricultural UniversityChangsha 410128China

The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.

关键词： Penicillium oxalicum WX-209 Crude enzyme Degradation Safety evaluation genome sequencing

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Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

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Asian Pacific Journal of Tropical Medicine 2023年第7期16卷 313-320页

作者： J.I.Abeynayake G.P.Chathuranga M.A.Y.Fernando M.K.Sahoo Department of Virology Medical Research InstituteP.O.Box:527Baseline RoadColombo 08Sri Lanka Department of Pathology Stanford University School of MedicinePalo AltoCaliforniaUnited States of America

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

关键词： Emerging SARS-CoV-2 variants Laboratory surveillance Nanopore technology genome sequencing Bioinformatics analysis and phylogeny Sociodemographic and sample cutoff(Ct)threshold Global sharing of genomic data/GISAID

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genome sequencing of the bacterial blight pathogen DY89031 reveals its diverse virulence and origins of Xanthomonas oryzae pv.oryzae strains

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Science China(Life Sciences) 2021年第12期64卷 2175-2185页

作者： Fudan Chen Bingxiao Yan Xiangyu Gong Helin Li Zuhua He College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China University of Chinese Academy of Sciences Beijing 100049China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China School of Life Sciences Henan UniversityKaifeng 475004China

The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pathogenesis,we performed genome sequencing of the Korea race 1 strain DY89031(J18)and analyzed the phylogenetic tree of 63 Xoo strains.We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions.Further,virulence effector proteins secreted by the type III secretion system(T3SS)of Xoo showed pathogenesis divergence.The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A,which is avirulent to rice Xa21,a well-known disease resistance(R)gene that can be broken down by DY89031.Interestingly,plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL(transcription activator-like)and non-TAL effectors that may support DY89031-specific virulence.Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.

关键词： DY89031 genome sequencing TAL effectors non-TAL effectors Xanthomonas oryzae pv.Oryzae

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genome sequencing Reveals the Role of MADS-box Gene Families in the Floral Morphology Evolution of Orchids

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Horticultural Plant Journal 2019年第6期5卷 247-254页

作者： Hsiangchia Lu Zhongjian Liu Siren Lan Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China

Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium.In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species(~ 20 000) than Apostasioideae(16 species). genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.

关键词： Orchid genome sequencing evolution development MADS-box gene family angiosperm

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Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

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Journal of Genetics and Genomics 2011年第1期38卷 47-53页

作者： Tae-Ho Park Beom-Seok Park Jin-A Kim Joon Ki Hong Mina Jin Young-Joo Seol Jeong-Hwan Mun Genomics and Functional Bio-Material Division National Academy of Agricultural ScienceRural Development Administration The Department of Horticultural Science Daegu University

As a part of the Multinational genome sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.

关键词： Brassica rapa Chinese cabbage Fosmid library genome sequencing Physical contig

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genome sequencing of moso bamboo(Phyllostachys heterocycla cv.pubescens)

Genome sequencing of moso bamboo(Phyllostachys heterocycla c...

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第十四届全国植物基因组学大会

作者： Zhenhua Peng Ying Lu Bin Han Zehui Jiang Research Institute of Forestry Chinese Academy of ForestryKey Laboratory of Tree Breeding and CultivationState Forestry Administration National Center for Gene Research Shanghai Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of Sciences International Center for Bamboo and Rattan

Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world.Bamboos belong to the subfamily Bambusoideae and are woody members... 详细信息

关键词： genome sequencing moso bamboo gramineae

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A chromosome-level genome assembly reveals that tandem-duplicated CYP706V oxidase genes control oridonin biosynthesis in the shoot apex of Isodon rubescens

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Molecular Plant 2023年第3期16卷 517-532页

作者： Yuwei Sun Jie Shao Haili Liu Hua Wang Guangyi Wang Jianhua Li Yaping Mao Zhuo Chen Ke Ma Lin Xu Yong Wang CAS-Key LaboratoryofSynthetic Bioogy CAS Center forEcellenceinMolecular Plant SciencesInsttuteof Plant Physioogy andEoogyChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100039China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China

The ent-kaurenoids(e.g.,oridonin and enmein)from the Isodon genus(Lamiaceae)are one class of diterpenoids with rich structural diversity and intriguing pharmaceutical activity.In contrast to the well-established gibberellin pathway,oxidative modifications diversifying the ent-kaurene skeleton in Isodon have remained undetermined for half a century.Here we report a chromosome-level genome assembly of I.rubescens,a well-recognized oridonin producer long favored by Asian people as a traditional herb with antitumor effects.The shoot apex was confirmed to be the actual region actively producing ent-kaurene diterpenoids.Through comparative genomics and phylogenetic analyses,we discovered a cluster of tandem-duplicated CYP706V oxygenase-encoding genes located on an ancient genomic block widely distributed in eudicots,whereas almost exclusively emerged in Isodon plants.In the shoot apex,IrCYP706V2 and IrCYP706V7 oxidized the ent-kaurene core in the initial stage of oridonin biosynthesis.Loss of CYP706Vs in other Lamiaceae plants offered an explanation for the specific kaurenoid production in Isodon plants.Moreover,we found that the Isodon genomes encode multiple diterpenoid synthases that are potentially involved in generating diterpenoid diversity.These findings provided new insights into the evolution of the lineage-specific diterpenoid pathway and laid a foundation for improving production of bioactive ent-kaurene-type diterpenoids by molecular breeding and synthetic biology approaches.

关键词： oridonin biosynthesis Isodon rubescens genome sequencing CYP706 oxidases diterpenoid diversity

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Weed genomics:yielding insights into the genetics of weedy traits for crop improvement

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aBIOTECH 2023年第1期4卷 20-30页

作者： Yujie Huang Dongya Wu Zhaofeng Huang Xiangyu Li Aldo Merotto Jr Lianyang Bai Longjiang Fan Institute of Crop Science and Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China Institute of Plant Protection Chinese Academy of Agricultural SciencesBeijing 100193China Department of Crop Sciences Agricultural School Federal University of Rio Grande do SulPorto Alegre 91540-000Brazil Hunan Weed Science Key Laboratory Hunan Academy of Agriculture SciencesChangshang 410125China

Weeds cause tremendous economic and ecological damage worldwide.The number of genomes established for weed species has sharply increased during the recent decade,with some 26 weed species having been sequenced and de novo genomes assembled.These genomes range from 270 Mb(Barbarea vulgaris)to almost 4.4 Gb(Aegilops tauschii).Importantly,chromosome-level assemblies are now available for 17 of these 26 species,and genomic investigations on weed populations have been conducted in at least 12 species.The resulting genomic data have greatly facilitated studies of weed management and biology,especially origin and evolution.Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement.In this review,we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.

关键词： Weeds genome sequencing Population genomics Adaptive traits Evolution

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