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Chromosome-level genome assembly of Cylas formicarius provides insights into its adaptation and invasion mechanisms

Journal of Integrative Agriculture 2023年第3期22卷 825-843页

作者： HUA Jin-feng ZHANG Lei HAN Yong-hua GOU Xiao-wan CHEN Tian-yuan HUANG Yong-mei LI Yan-qing MA Dai-fu LI Zong-yun Institute of Integrative Plant Biology/Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics/School of Life Sciences Jiangsu Normal UniversityXuzhou 221116P.R.China Sweet Potato Laboratory Institute of Maize ResearchGuangxi Academy of Agricultural SciencesNanning 530007P.R.China Xuzhou Academy of Agricultural Sciences/Institute of Sweet Potato Research Chinese Academy of Agricultural SciencesXuzhou 221131P.R.China

Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic *** study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. *** Illumina and pacbio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 *** high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, *** total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated *** genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory *** further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other *** high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.

关键词： Cylas formicarius pacbio sequencing high-through chromosome conformation capture chromosome-level genome chemosensory genes fluorescence competitive binding

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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

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Fungal Diversity 2021年第6期111卷 573-588页

作者： Leho Tedersoo Vladimir Mikryukov Sten Anslan Mohammad Bahram Abdul Nasir Khalid Adriana Corrales Ahto Agan Aída-M.Vasco-Palacios Alessandro Saitta Alexandre Antonelli Andrea C.Rinaldi Annemieke Verbeken Bobby P.Sulistyo Boris Tamgnoue Brendan Furneaux Camila Duarte Ritter Casper Nyamukondiwa Cathy Sharp César Marín D.Q.Dai Daniyal Gohar Dipon Sharmah Elisabeth Machteld Biersma Erin K.Cameron Eske De Crop Eveli Otsing Evgeny A.Davydov Felipe E.Albornoz Francis Q.Brearley Franz Buegger Genevieve Gates Geoffrey Zahn Gregory Bonito Indrek Hiiesalu Inga Hiiesalu Irma Zettur Isabel C.Barrio Jaan Pärn Jacob Heilmann-Clausen Jelena Ankuda John Y.Kupagme Joosep Sarapuu Jose G.Maciá-Vicente Joseph Djeugap Fovo József Geml Juha M.Alatalo Julieta Alvarez-Manjarrez Jutamart Monkai Kadri Põldmaa Kadri Runnel Kalev Adamson Kari A.Bråthen Karin Pritsch Kassim I.Tchan Kęstutis Armolaitis Kevin D.Hyde Kevin K.Newsham Kristel Panksep Lateef A.Adebola Louis J.Lamit Malka Saba Marcela Eda Silva Cáceres Maria Tuomi Marieka Gryzenhout Marijn Bauters Miklós Bálint Nalin Wijayawardene Niloufar Hagh-Doust Nourou S.Yorou Olavi Kurina Peter E.Mortimer Peter Meidl RHenrik Nilsson Rasmus Puusepp Rebeca Casique-Valdés Rein Drenkhan Roberto Garibay-Orijel Roberto Godoy Saleh Alfarraj Saleh Rahimlou Sergei Põlme Sergey V.Dudov Sunil Mundra Talaat Ahmed Tarquin Netherway Terry W.Henkel Tomas Roslin Vladimir E.Fedosov Vladimir G.Onipchenko WAErandi Yasanthika Young Woon Lim Meike Piepenbring Darta Klavina Urmas Kõljalg Kessy Abarenkov Mycology and Microbiology Center University of TartuTartuEstonia Institute of Ecology and Earth Sciences TartuEstonia Department of Ecology Swedish University of Agricultural SciencesUppsalaSweden Department of Botany University of the PunjabQuaid-e-Azam CampusLahorePakistan Centro de Investigaciones en Microbiología y Biotecnología-UR(CIMBIUR) Facultad de Ciencias NaturalesUniversidad del RosarioBogotáColombia Grupo de Microbiología Ambiental y BioMicro Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellínColombia Department of Agricultural Food and Forest SciencesUniversity of PalermoPalermoItaly Royal Botanic Gardens SurreyUK Department of Biomedical Sciences University of CagliariCagliariItaly Research Group Mycology Department of BiologyGhent UniversityGhentBelgium Department of Biomedicine Indonesia International Institute for Life SciencesJakartaIndonesia Plant Pathology and Agricultural Zoology Research Unit Department of Plant ProtectionFaculty of Agronomy and Agricultural SciencesUniversity of DschangDschangCameroon Department of Ecology and Genetics Uppsala UniversityUppsalaSweden Eukaryotic Microbiology University of Duisburg-EssenEssenGermany Department of Biological Sciences and Biotechnology Botswana International University of Science and TechnologyPalapyeBotswana Natural History Museum of Zimbabwe BulawayoZimbabwe Institute of Botany Czech Academy of SciencesPrůhoniceCzech Republic Center for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujingPeople’s Republic of China Department of Botany Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia British Antarctic Survey NERCCambridgeUK Natural History Museum of Denmark University of CopenhagenCopenhagenDenmark Department of Environmental Science Saint Mary’s UniversityHalifaxNSCanada Altai State University BarnaulRussia CSIRO Land and Water WembleyWAAustralia Department of N

Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and *** data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and *** dataset comprises 722,682 fungal operational taxonomic units(OTUs)derived from pacbio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all *** plots are supplied with geographical and edaphic *** OTUs are taxonomically and functionally assigned to guilds and other functional *** entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential *** dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published *** GSMc dataset is available over the PlutoF repository.

关键词： Soil fungi Global dataset pacbio sequencing Fungal richness

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Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

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Fungal Diversity 2020年第4期103卷 273-293页

作者： Leho Tedersoo Sten Anslan Mohammad Bahram Urmas Kõljalg Kessy Abarenkov Institute of Ecology and Earth Sciences Tartu University14a Ravila50411 TartuEstonia Zoological Institute Braunschweig University of TechnologyMendelssohnstr.438106 BrunswickGermany Department of Ecology Swedish University of Agricultural SciencesUlls väg 1675651 UppsalaSweden Natural History Museum of Tartu University 14a Ravila50411 TartuEstonia

Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic *** study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads ofsequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.I

关键词： Soil fungi Top 50 most wanted fungi Phylogenetic diversity pacbio sequencing 18S rRNA gene(small subunit) 28S rRNA gene(large subunit)

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Microbiome Diversity Analysis of the Bacterial Community in Idah River, Kogi State, Nigeria

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Advances in Microbiology 2022年第5期12卷 343-362页

作者： Deborah Ebunoluwa Adedire Adijat Ozohu Jimoh Zainab Kashim-Bello Bilyaminu Adam Wase Shuaibu Oluwabukola Atinuke Popoola Kabiru Isa Pate Onyinye Stainless Uzor Eno Etingwa Jumoke Florence Joda Oyetola Olanrewaju Opaleye Victoria Adejoke Ogunlowo Kehinde Rukayyat Adeniran Oyekanmi Nashiru Genetics Genomics and Bioinformatics Department National Biotechnology Development Agency Abuja Nigeria Aquatic Bioresources Training Center National Biotechnology Development Agency Idah Kogi Nigeria Aquatic Bioresources Training Center National Biotechnology Development Agency Tunari Taraba Nigeria Center for Genomics Research and Innovation National Biotechnology Development Agency Abuja Nigeria

The analysis of bacterial diversity in aquatic systems particularly in rivers, lakes, and streams can provide useful data on the effect of anthropogenic activities on such water bodies to humans and fishes. Idah River, the focal point of this study, is an offshoot of the two major Nigerian rivers characterized by observed human activities and pollution sources. Water samples were collected from four designated sites and assessed for their bacterial assemblages and structure, using pacbio Single-Molecule Real-Time (SMRT) sequencing technology. The full length of the 16S rRNA gene was sequenced, and Amplicon Sequence Variants were generated using the DADA2 workflow optimised for pacbio long-read amplicons in Rstudio. A total of 8751 high-quality reads obtained were taxonomically classified as 24 phyla, 42 classes, 84 orders, 125 families, 156 genera, and 106 species. Taxonomical composition revealed Proteobacteria as the most abundant phyla across all sample sites. At the genera level, Azospira (57.03%) was the most dominant ASV in Docking Point A, while Acinetobacter (66.67%) was the most abundant ASV in Docking Point B. In Idah Axis Confluence, hgcl clade (65.66%) was the most prevalent ASV, whereas Holophaga (42.86%) was the most common ASV in Idah Axis Midstream. Genera analysis also revealed that 12.9% of the total ASVs were discovered across all sample sites. Among these were pathogenic bacteria, reducers, and degraders of domestic and animal wastes. Observed results provide evidence that sampled sites of Idah River are contaminated, most likely through constant human activities and thus, could have an impact on resident fishes as well. This study, therefore, agrees with a previous report from the river, which used standard microbial procedures. However, next-generation sequencing techniques employed revealed more bacterial community than the former, including unresolved taxonomic sequences that may be novel.

关键词： Idah River Dada2 pacbio sequencing Bacterial Diversity Amplicon Sequence Variants

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Improved de novo genome assembly and analysis of the apicomplexan parasite Eimeria maxima

Improved de novo genome assembly and analysis of the apicomp...

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第十一届全国寄生虫学青年工作者学术研讨会

作者： Dandan Hu Chaoyue Wang Miner Deng Si Wang Sixin Zhang Chunhui Duan Xinming Tang Jingxia Suo Xun Suo Xianyong Liu National Animal Protozoa Laboratory College of Veterinary MedicineChina Agricultural University

Eimeria maxima is a pathogenic eimerian parasite in chickens and is a major causative agent of chicken coccidiosis,which could lead to huge economic losses in the poultry *** the genome of *** helps us to control this *** genomes of *** Weybridge strain had been sequenced using Illumima sequencing with a single ***,this genome was too fragmented so that it cannot fulfill the urgent needs in playing a reference role in resequencing ***,we performed a de novo genome assembly for the *** Beijing strain by single molecule real time sequencing(SMRT).After Pac Bio sequencing,over 689 thousand clean reads(6.2 Gb clean data,mean reads length = 9 kb) were assembled into a 52 Mb genome by the combination of Canu and wtdbg *** new assembled *** genome consisted of 55 contigs and the contig N50 reached 2.2 Mb,which showed great improvement compared to the old version(4570 contigs,N50 = 21 kb).Prediction shows that the genome of *** Beijing strain contains 7222 protein coding genes with average gene length of 3412 bp(average exon length = 2106 bp).A total of 19.65 Mb(37.78%) repeat sequences were found in the genome,indicating that the *** Beijing strain had a highly repeated genome structure as other sequenced Eimeria *** interestingly,we found no micro RNA in the *** genome,which was a common phenomenon exists in Eimeria and Plasmodium *** high-quality reference genome of *** will promote the genetic and biological studies in Eimeria.

关键词： Eimeria maxima genome pacbio sequencing

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