1
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Pan M, Shi H, Qi T, Cai L, Ge Q. The biological characteristics of long cell-free DNA in spent embryos culture medium as noninvasive biomarker in in-vitro embryo selection. Gene 2024; 927:148667. [PMID: 38857715 DOI: 10.1016/j.gene.2024.148667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
An improved understanding of the cfDNA fragmentomics has proved it as a promising biomarker in clinical applications. However, biological characteristics of cfDNA in spent embryos culture medium (SECM) remain unsolved obstacles before the application in non-invasive in-vitro embryo selection. In this study, we developed a Tn5 transposase and ligase integrated dual-library construction sequencing strategy (TDual-Seq) and revealed the fragmentomic profile of cfDNA of all sizes in early embryonic development. The detected ratio of long cfDNA (>500 bp) was improved from 4.23 % by traditional NGS to 12.80 % by TDual-Seq. End motif analysis showed long cfDNA molecules have a more dominance of fragmentation intracellularly in apoptotic cells with higher predominance of G-end, while shorter cfDNA undergo fragmentation process both intracellularly and extracellularly. Moreover, the mutational pattern of cfDNA and the correlated GO biological process were well differentiated in cleavage and blastocyst embryos. Finally, we developed a multiparametric index (TQI) that employs the fragmentomic profiles of cfDNA, and achieved an area under the ROC curve of 0.927 in screening top quality embryos. TDual-Seq strategy has facilitated characterizing the fragmentomic profile of cfDNA of all sizes in SECM, which are served as a class of non-invasive biomarkers in the evaluation of embryo quality in in-vitro fertilization. And this improved strategy has opened up potential clinical utilities of long cfDNA analysis.
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Affiliation(s)
- Min Pan
- School of Medicine, Southeast University, Nanjing, China; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Huajuan Shi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ting Qi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lingbo Cai
- Clinical Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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2
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Law STS, Nong W, Li C, Chong TK, Yip HY, Swale T, Chiu SW, Chung RYN, Lam HM, Wong SYS, Wong H, Hui JHL. Genome of tropical bed bug Cimex hemipterus (Cimicidae, Hemiptera) reveals tetraspanin expanded in bed bug ancestor. INSECT SCIENCE 2024. [PMID: 38830803 DOI: 10.1111/1744-7917.13388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 06/05/2024]
Abstract
Cimex species are ectoparasites that exclusively feed on warm-blooded animals such as birds and mammals. Three cimicid species are known to be persistent pests for humans, including the tropical bed bug Cimex hemipterus, common bed bug Cimex lectularius, and Eastern bat bug Leptocimex boueti. To date, genomic information is restricted to the common bed bug C. lectularius, which limits understanding their biology and to provide controls of bed bug infestations. Here, a chromosomal-level genome assembly of C. hemipterus (495 Mb [megabase pairs]) contained on 16 pseudochromosomes (scaffold N50 = 34 Mb), together with 9 messenger RNA and small RNA transcriptomes were obtained. In comparison between hemipteran genomes, we found that the tetraspanin superfamily was expanded in the Cimex ancestor. This study provides the first genome assembly for the tropical bed bug C. hemipterus, and offers an unprecedented opportunity to address questions relating to bed bug infestations, as well as genomic evolution to hemipterans more widely.
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Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Chade Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Tze Kiu Chong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Siu Wai Chiu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Roger Yat-Nork Chung
- School of Public Health and Primary Care, CUHK Institute of Health Equity, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Samuel Y S Wong
- School of Public Health and Primary Care, CUHK Institute of Health Equity, The Chinese University of Hong Kong, Hong Kong, China
| | - Hung Wong
- Department of Social Work, CUHK Institute of Health Equity, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
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3
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Zhang Z, Xiao J, Wang H, Yang C, Huang Y, Yue Z, Chen Y, Han L, Yin K, Lyu A, Fang X, Zhang L. Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity. Nat Commun 2024; 15:4631. [PMID: 38821971 PMCID: PMC11143213 DOI: 10.1038/s41467-024-49060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 05/17/2024] [Indexed: 06/02/2024] Open
Abstract
Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.
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Grants
- This research was partially supported by the Young Collaborative Research Grant (C2004-23Y, L.Z.), HMRF (11221026, L.Z.), the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220012, L.Z.), the Hong Kong Research Grant Council Early Career Scheme (HKBU 22201419, L.Z.), HKBU Start-up Grant Tier 2 (RC-SGT2/19-20/SCI/007, L.Z.), HKBU IRCMS (No. IRCMS/19-20/D02, L.Z.).
- This research was partially supported by the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220014, KJ.Y.).
- The study were partially supported by the Science Technology and Innovation Committee of Shenzhen Municipality, China (SGDX20190919142801722, XD.F.),
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Affiliation(s)
- Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Jin Xiao
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Hongbo Wang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | | | - Zhen Yue
- BGI Research, Sanya, 572025, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
| | - Lijuan Han
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Kejing Yin
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiaodong Fang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Sanya, 572025, China
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China.
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4
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Chen M, Tan MH, Liu J, Yang YM, Yu JL, He LJ, Huang YZ, Sun YX, Qian YQ, Yan K, Dong MY. An efficient molecular genetic testing strategy for incontinentia pigmenti based on single-tube long fragment read sequencing. NPJ Genom Med 2024; 9:32. [PMID: 38811629 PMCID: PMC11137062 DOI: 10.1038/s41525-024-00421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/18/2024] [Indexed: 05/31/2024] Open
Abstract
Incontinentia pigmenti (IP) is a rare X-linked dominant neuroectodermal dysplasia that primarily affects females. The only known causative gene is IKBKG, and the most common genetic cause is the recurrent IKBKG△4-10 deletion resulting from recombination between two MER67B repeats. Detection of variants in IKBKG is challenging due to the presence of a highly homologous non-pathogenic pseudogene IKBKGP1. In this study, we successfully identified four pathogenic variants in four IP patients using a strategy based on single-tube long fragment read (stLFR) sequencing with a specialized analysis pipeline. Three frameshift variants (c.519-3_519dupCAGG, c.1167dupC, and c.700dupT) were identified and subsequently validated by Sanger sequencing. Notably, c.519-3_519dupCAGG was found in both IKBKG and IKBKGP1, whereas the other two variants were only detected in the functional gene. The IKBKG△4-10 deletion was identified and confirmed in one patient. These results demonstrate that the proposed strategy can identify potential pathogenic variants and distinguish whether they are derived from IKBKG or its pseudogene. Thus, this strategy can be an efficient genetic testing method for IKBKG. By providing a comprehensive understanding of the whole genome, it may also enable the exploration of other genes potentially associated with IP. Furthermore, the strategy may also provide insights into other diseases with detection challenges due to pseudogenes.
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Affiliation(s)
- Min Chen
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Mei-Hua Tan
- BGI Genomics, Shenzhen, Guangdong, 518083, P. R. China
| | - Jiao Liu
- Lishui Maternity and Child Health Care Hospital, Lishui, Zhejiang, 323000, P. R. China
| | - Yan-Mei Yang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Jia-Ling Yu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Li-Juan He
- BGI Genomics, Shenzhen, Guangdong, 518083, P. R. China
| | - Ying-Zhi Huang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Yi-Xi Sun
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Ye-Qing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Kai Yan
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China
| | - Min-Yue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, P. R. China.
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, Zhejiang, 310006, P. R. China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, Zhejiang, 310006, P. R. China.
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5
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Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024; 14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA.
| | - Yasmin Rajendran
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | | | - Maria Arvio
- Päijät-Häme Wellbeing Services, Neurology, Lahti, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Kristiina Avela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Johanna Granvik
- The Wellbeing Services County of Ostrobothnia, Kokkola, Finland
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Tuomo Määttä
- The Wellbeing Services County of Kainuu, Kajaani, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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6
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Cai Y, Anderson E, Xue W, Wong S, Cui L, Cheng X, Wang O, Mao Q, Liu SJ, Davis JT, Magalang PR, Schmidt D, Kasuga T, Garbelotto M, Drmanac R, Kua CS, Cannon C, Maloof JN, Peters BA. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3 (BETHESDA, MD.) 2024; 14:jkae043. [PMID: 38427916 PMCID: PMC11075539 DOI: 10.1093/g3journal/jkae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome, enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.
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Affiliation(s)
- Ying Cai
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Ellis Anderson
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Wen Xue
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sylvia Wong
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Luman Cui
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofang Cheng
- Department of Research, MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ou Wang
- Department of Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Mao
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Sophie Jia Liu
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - John T Davis
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Paulo R Magalang
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Douglas Schmidt
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service, Davis, CA 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
| | - Chai-Shian Kua
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Charles Cannon
- Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA
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7
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Ewart KM, Ho SYW, Chowdhury AA, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc Biol Sci 2024; 291:20232439. [PMID: 38772424 DOI: 10.1098/rspb.2023.2439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024] Open
Abstract
Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to reductions in effective population size, rather than gene-specific effects (e.g. indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging of deleterious alleles at the colony level. Additionally, we identified genomic adaptations that may underpin caste differentiation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Frederick R Jaya
- Ecology & Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Okinawa International University, Okinawa, Japan
| | - Juno Bennett
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Harley A Rose
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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8
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Li H, Durbin R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet 2024:10.1038/s41576-024-00718-w. [PMID: 38649458 DOI: 10.1038/s41576-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly - the process of reconstructing the genome sequence of an organism from sequencing reads - has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome - also known as telomere-to-telomere assembly - for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.
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Affiliation(s)
- Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Richard Durbin
- Department of Genetics, Cambridge University, Cambridge, UK.
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9
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Paasch A, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method. Sci Rep 2024; 14:7988. [PMID: 38580715 PMCID: PMC10997766 DOI: 10.1038/s41598-024-58733-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Peter L Chang
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Amber Paasch
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA.
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10
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Dong Z, Wang J, Chen G, Guo Y, Zhao N, Wang Z, Zhang B. A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis. Sci Data 2024; 11:322. [PMID: 38548787 PMCID: PMC10978949 DOI: 10.1038/s41597-024-03173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.
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Affiliation(s)
- Zhongdian Dong
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiangman Wang
- Qingdao Marine Management Support Center, Qingdao, Shandong, China
| | - Guozhu Chen
- National Plateau Wetland Research Center, College of Wetlands, Southwest Forestry University, Kunming, 650224, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Na Zhao
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory-Zhanjiang, Zhanjiang, 524000, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Bo Zhang
- Key Laboratory of Aquaculture in the South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory-Zhanjiang, Zhanjiang, 524000, China.
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11
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Zhang H, Liu P, Zhang Y, Sun H, Wang Y, Gao Z, Liu X. Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny. BMC Genom Data 2024; 25:34. [PMID: 38528505 PMCID: PMC10962098 DOI: 10.1186/s12863-024-01222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Calamus tetradactylus, a species primarily distributed in Vietnam, Laos, and southern China, is highly valued for its utilization as a small-diameter rattan material. While its physical and mechanical properties have been extensively studied, the genomic characteristics of C. tetradactylus remain largely unexplored. RESULTS To gain a better understanding of its chloroplast genomic features and evolutionary relationships, we conducted sequencing and assembly of the chloroplast genome of C. tetradactylus. The complete chloroplast genome exhibited the typical highly conserved quartile structure, with specific variable regions identified in the single-copy region (like psbF-psbE, π = 0.10327, ndhF-rpl32, π = 0.10195), as well as genes such as trnT-GGU (π = 0.05764) and ycf1 (π = 0.03345) and others. We propose that these regions and genes hold potential as markers for species identification. Furthermore, phylogenetic analysis revealed that C. tetradactylus formed a distinct clade within the phylogenetic tree, alongside other Calamus species, and C. tetradactylus was most closely related to C. walkeri, providing support for the monophyly of the genus. CONCLUSION The analysis of the chloroplast genome conducted in this study provides valuable insights that can contribute to the improvement of rattan breeding programs and facilitate sustainable development in the future.
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Affiliation(s)
| | - Peng Liu
- BGI Research, Beijing, 102601, China
| | - Yi Zhang
- School of nursing, Chongqing Medical and Pharmaceutical College, P. R, Chongqing, China
| | - Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Yue Wang
- BGI Research, Beijing, 102601, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Xin Liu
- BGI Research, Beijing, 102601, China.
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Pootakham W, Somta P, Kongkachana W, Naktang C, Sonthirod C, U-Thoomporn S, Yoocha T, Phadphon P, Tangphatsornruang S. A de novo chromosome-scale assembly of the Lablab purpureus genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1347744. [PMID: 38504891 PMCID: PMC10948561 DOI: 10.3389/fpls.2024.1347744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024]
Abstract
Introduction Lablab (Lablab purpureus (L.) Sweet), an underutilized tropical legume crop, plays a crucial role in global food and nutritional security. To enhance our understanding of its genetic makeup towards developing elite cultivars, we sequenced and assembled a draft genome of L. purpureus accession PK2022T020 using a single tube long fragment read (stLFR) technique. Results and discussion The preliminary assembly encompassed 367 Mb with a scaffold N50 of 4.3 Mb. To improve the contiguity of our draft genome, we employed a chromatin contact mapping (Hi-C) approach to obtain a pseudochromosome-level assembly containing 366 Mb with an N50 length of 31.1 Mb. A total of 327.4 Mb had successfully been anchored into 11 pseudomolecules, corresponding to the haploid chromosome number in lablab. Our gene prediction recovered 98.4% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses utilizing sequence information from single-copy orthologous genes demonstrated that L. purpureus diverged from the last common ancestor of the Phaseolus/Vigna species approximately 27.7 million years ago. A gene family expansion analysis revealed a significant expansion of genes involved in responses to biotic and abiotic stresses. Our high-quality chromosome-scale reference assembly provides an invaluable genomic resource for lablab genetic improvement and future comparative genomics studies among legume species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Wasitthee Kongkachana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Poompat Phadphon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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13
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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14
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Niu X, Lv Y, Chen J, Feng Y, Cui Y, Lu H, Liu H. The genome assembly and annotation of the white-lipped tree pit viper Trimeresurus albolabris. GIGABYTE 2024; 2024:gigabyte106. [PMID: 38313188 PMCID: PMC10836062 DOI: 10.46471/gigabyte.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.
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Affiliation(s)
- Xiaotong Niu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- School of Ecology, Sun Yat-sen University, Shenzhen, 510275, China
| | - Yakui Lv
- College of Ecology and Environment, Hainan University, Haikou, 570228, China
| | - Jin Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yueheng Feng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
| | - Yilin Cui
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, 570228, China
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15
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Lauschke VM, Zhou Y, Ingelman-Sundberg M. Pharmacogenomics Beyond Single Common Genetic Variants: The Way Forward. Annu Rev Pharmacol Toxicol 2024; 64:33-51. [PMID: 37506333 DOI: 10.1146/annurev-pharmtox-051921-091209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Interindividual variability in genes encoding drug-metabolizing enzymes, transporters, receptors, and human leukocyte antigens has a major impact on a patient's response to drugs with regard to efficacy and safety. Enabled by both technological and conceptual advances, the field of pharmacogenomics is developing rapidly. Major progress in omics profiling methods has enabled novel genotypic and phenotypic characterization of patients and biobanks. These developments are paralleled by advances in machine learning, which have allowed us to parse the immense wealth of data and establish novel genetic markers and polygenic models for drug selection and dosing. Pharmacogenomics has recently become more widespread in clinical practice to personalize treatment and to develop new drugs tailored to specific patient populations. In this review, we provide an overview of the latest developments in the field and discuss the way forward, including how to address the missing heritability, develop novel polygenic models, and further improve the clinical implementation of pharmacogenomics.
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Affiliation(s)
- Volker M Lauschke
- Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden;
- Tübingen University, Tübingen, Germany
| | - Yitian Zhou
- Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden;
- Tübingen University, Tübingen, Germany
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16
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Yang C, Zhang Z, Huang Y, Xie X, Liao H, Xiao J, Veldsman WP, Yin K, Fang X, Zhang L. LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome. Gigascience 2024; 13:giae028. [PMID: 38869148 PMCID: PMC11170215 DOI: 10.1093/gigascience/giae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/15/2024] [Accepted: 05/09/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Linked-read sequencing technologies generate high-base quality short reads that contain extrapolative information on long-range DNA connectedness. These advantages of linked-read technologies are well known and have been demonstrated in many human genomic and metagenomic studies. However, existing linked-read analysis pipelines (e.g., Long Ranger) were primarily developed to process sequencing data from the human genome and are not suited for analyzing metagenomic sequencing data. Moreover, linked-read analysis pipelines are typically limited to 1 specific sequencing platform. FINDINGS To address these limitations, we present the Linked-Read ToolKit (LRTK), a unified and versatile toolkit for platform agnostic processing of linked-read sequencing data from both human genome and metagenome. LRTK provides functions to perform linked-read simulation, barcode sequencing error correction, barcode-aware read alignment and metagenome assembly, reconstruction of long DNA fragments, taxonomic classification and quantification, and barcode-assisted genomic variant calling and phasing. LRTK has the ability to process multiple samples automatically and provides users with the option to generate reproducible reports during processing of raw sequencing data and at multiple checkpoints throughout downstream analysis. We applied LRTK on linked reads from simulation, mock community, and real datasets for both human genome and metagenome. We showcased LRTK's ability to generate comparative performance results from preceding benchmark studies and to report these results in publication-ready HTML document plots. CONCLUSIONS LRTK provides comprehensive and flexible modules along with an easy-to-use Python-based workflow for processing linked-read sequencing datasets, thereby filling the current gap in the field caused by platform-centric genome-specific linked-read data analysis tools.
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Affiliation(s)
- Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
| | - Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
| | - Yufen Huang
- BGI Research, Shenzhen 518083, China
- BGI Genomics, Shenzhen 518083, China
| | | | - Herui Liao
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR 999077, Hong Kong
| | - Jin Xiao
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
| | - Werner Pieter Veldsman
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
| | - Kejing Yin
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
| | - Xiaodong Fang
- BGI Genomics, Shenzhen 518083, China
- BGI Research, Sanya 572025, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
- Institute for Research and Continuing Education, Hong Kong Baptist University, Hong Kong SAR 999077, Hong Kong
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17
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Höjer P, Frick T, Siga H, Pourbozorgi P, Aghelpasand H, Martin M, Ahmadian A. BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies. Nucleic Acids Res 2023; 51:e114. [PMID: 37941142 PMCID: PMC10711428 DOI: 10.1093/nar/gkad1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10× Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (∼10×) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10× Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.
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Affiliation(s)
- Pontus Höjer
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Tobias Frick
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Humam Siga
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Parham Pourbozorgi
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Hooman Aghelpasand
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Marcel Martin
- Stockholm University, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Afshin Ahmadian
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
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18
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Niu X, Lu H, Shi M, Wang S, Zhou Y, Liu H. Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus. GIGABYTE 2023; 2023:gigabyte97. [PMID: 38023064 PMCID: PMC10644238 DOI: 10.46471/gigabyte.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
The Brown-Spotted Pit viper (Protobothrops mucrosquamatus), also known as the Chinese habu, is a widespread and highly venomous snake distributed from Northeastern India to Eastern China. Genomics research can contribute to our understanding of venom components and natural selection in vipers. Here, we collected, sequenced and assembled the genome of a male P. mucrosquamatus individual from China. We generated a highly continuous reference genome, with a length of 1.53 Gb and 41.18% of repeat elements content. Using this genome, we identified 24,799 genes, 97.97% of which could be annotated. We verified the validity of our genome assembly and annotation process by generating a phylogenetic tree based on the nuclear genome single-copy genes of six other reptile species. The results of our research will contribute to future studies on Protobothrops biology and the genetic basis of snake venom.
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Affiliation(s)
- Xiaotong Niu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- School of Ecology, Sun Yat-sen University, Shenzhen, 510275, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
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19
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Guo M, Songyang Z, Xiong Y. ChArmTelo Enables Large-Scale Chromosome Arm-Level Telomere Analysis across Human Populations and in Cancer Patients. SMALL METHODS 2023; 7:e2300385. [PMID: 37526331 DOI: 10.1002/smtd.202300385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Indexed: 08/02/2023]
Abstract
Telomeres are structures protecting chromosome ends. However, a scalable and cost-effective method to investigate chromosome arm-level (ChArm) telomeres (Telos) in large-scale projects is still lacking, hindering intensive investigation of high-resolution telomeres across cancers and other diseases. Here, ChArmTelo, the first computational toolbox to analyze telomeres at chromosome arm level in human and other animal species, using 10X linked-read and similar technologies, is presented. ChArmTelo currently consists of two algorithms, TeloEM and TeloKnow, for arm-level telomere length (TL) analysis. The algorithms are demonstrated by comprehensive analysis of chromosome arm-level telomere lengths (chArmTLs) in nearly 400 whole genome sequencing samples (WGS) from human populations and animals, including healthy and cancer samples. Notably, considerable performance improvement contributed by using the latest complete telomere-to-telomere reference genome (CHM13v2), compared to hg38, is shown. ChArmTelo reveals population-specific chArmTL differences and liver cancer signatures of chArmTLs and that DNA replication origin disruption may contribute to cancer by affecting TLs. Importantly, ChArmTelo can be readily applied to tens of thousands of cancer and healthy samples with published WGS data.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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20
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Guerreiro R, Bonthala VS, Schlüter U, Hoang NV, Triesch S, Schranz ME, Weber APM, Stich B. A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe. PLANT, CELL & ENVIRONMENT 2023; 46:3611-3627. [PMID: 37431820 DOI: 10.1111/pce.14662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.
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Affiliation(s)
- Ricardo Guerreiro
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Urte Schlüter
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nam V Hoang
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Sebastian Triesch
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
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21
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Xiong Z, He D, Guang X, Li Q. Novel tRNA Gene Rearrangements in the Mitochondrial Genomes of Poneroid Ants and Phylogenetic Implication of Paraponerinae (Hymenoptera: Formicidae). Life (Basel) 2023; 13:2068. [PMID: 37895449 PMCID: PMC10608118 DOI: 10.3390/life13102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Ants (Formicidae) are the most diverse eusocial insects in Hymenoptera, distributed across 17 extant subfamilies grouped into 3 major clades, the Formicoid, Leptanilloid, and Poneroid. While the mitogenomes of Formicoid ants have been well studied, there is a lack of published data on the mitogenomes of Poneroid ants, which requires further characterization. In this study, we first present three complete mitogenomes of Poneroid ants: Paraponera clavata, the only extant species from the subfamily Paraponerinae, and two species (Harpegnathos venator and Buniapone amblyops) from the Ponerinae subfamily. Notable novel gene rearrangements were observed in the new mitogenomes, located in the gene blocks CR-trnM-trnI-trnQ-ND2, COX1-trnK-trnD-ATP8, and ND3-trnA-trnR-trnN-trnS1-trnE-trnF-ND5. We reported the duplication of tRNA genes for the first time in Formicidae. An extra trnQ gene was identified in H. venator. These gene rearrangements could be explained by the tandem duplication/random loss (TDRL) model and the slipped-strand mispairing model. Additionally, one large duplicated region containing tandem repeats was identified in the control region of P. clavata. Phylogenetic analyses based on protein-coding genes and rRNA genes via maximum likelihood and Bayes methods supported the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae. However, caution is advised in interpreting the positions of Paraponerinae due to the potential artifact of long-branch attraction.
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Affiliation(s)
- Zijun Xiong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
| | - Ding He
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | | | - Qiye Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
- BGI Research, Shenzhen 518083, China;
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22
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Lai Z, Afriyie G, Cui H, Chen L, Xu Z, Chen Z, Liang Q, Luo J, Dong Z, Shao C, Guo Y, Wang Z. The First High-Quality Chromosome-Level Genome of the Lutjanus erythropterus (Bloch, 1790) Using Single-Tube Long Fragment Reads and Hi-C Technologies. Genome Biol Evol 2023; 15:evad171. [PMID: 37768150 PMCID: PMC10558211 DOI: 10.1093/gbe/evad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Lutjanus erythropterus (Bloch, 1790), a Perciformes from the Lutjanidae family, is a commercially important species because of its taste and abundance. Despite the increase in genome resources in recent years, few genome assemblies are available within this fish family for comparative and functional studies. In this study, we determined the chromosomal genome of Crimson snapper using high-throughput Single-Tube Long Fragment Reads sequencing technology and Hi-C data. The final assembly size was 973.04 Mb with contig and scaffold N50 values of 1.51 and 40.65 Mb, respectively. We successfully scaffolded 95.84% of the genome sequence onto 24 chromosomes ranging in length from 19.37 to 49.48 Mb. A total of 22,663 genes and 13,877 gene families were identified in the genome, with 29 gene families being L. erythropterus-specific. A phylogenetic analysis using single-copy gene families showed that L. erythropterus and Larimichthys crocea had the closest genetic relationship with a divergence time of ∼47.7 Ma. This new genomic resource will facilitate comparative genomic studies as well as genetic breeding programs for L. erythropterus.
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Affiliation(s)
- Zhuoxin Lai
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Haitao Cui
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Lujun Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhenmin Xu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zizhao Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Quilu Liang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jie Luo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong, China
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23
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Yang X, Song Y, Zhang R, Yu M, Guo X, Guo H, Du X, Sun S, Li C, Mao X, Fan G, Liu X. Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes. DNA Res 2023; 30:dsad022. [PMID: 37788574 PMCID: PMC10590162 DOI: 10.1093/dnares/dsad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.
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Affiliation(s)
- Xianwei Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Song
- BGI Research, Qingdao 266555, China
| | | | | | | | | | - Xiao Du
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Shuai Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Qingdao 266555, China
| | | | | | - Guangyi Fan
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Xin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
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24
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Zhang S, Song Y, Liu M, Yuan Z, Zhang M, Zhang H, Seim I, Fan G, Liu S, Liu X. Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits. DNA Res 2023; 30:dsad018. [PMID: 37590994 PMCID: PMC10468729 DOI: 10.1093/dnares/dsad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 08/19/2023] Open
Abstract
Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average genome size of 65,611 Mb. Chelmon rostratus, comprising 24 chromosomes assembled to the chromosome level, could be served as a reference genome for butterflyfish. By conducting a collinearity analysis between butterflyfishes and several fishes, we elucidated the specific and conserved genomic features of butterflyfish, with particular emphasis on novel genes arising from tandem duplications and their potential functions. In addition to the two melanocyte-specific tyr genes commonly found in fish, we found the gene tyrp3, a new tyrosinase-related proteins gene in the reef fish, including butterflyfish and clownfish, implicating their involvement in the pigmentation diversity of fish. Additionally, we observed a tandem duplication expansion of three copies of nell1 gene in C. rostratus genome, which likely contribute to its unique jaw development and distinctive morphology of its sharp mouth. These results provided valuable genomic resources for further investigations into the genetic diversity and evolutionary adaptations of reef fish.
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Affiliation(s)
- Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Queensland, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
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25
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Baker JL. Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiol Rev 2023; 47:fuad051. [PMID: 37667515 PMCID: PMC10503653 DOI: 10.1093/femsre/fuad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/02/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.
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Affiliation(s)
- Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, School of Dentistry, Oregon Health & Science University, 3181 Sam Jackson Park Road, Portland, OR 97202, United States
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA 92093, United States
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26
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Li X, Wang P, Pan Q, Liu G, Liu W, Omotoso O, Du J, Li Z, Yu Y, Huang Y, Zhu P, Li M, Zhou X. Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance. Aging Cell 2023; 22:e13917. [PMID: 37395176 PMCID: PMC10497851 DOI: 10.1111/acel.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
The naked mole rat (Heterocephalus glaber), bats (e.g., genus Myotis), and elephants (family Elephantidae) are known as long-lived mammals and are assumed to be excellent cancer antagonists. However, whether there are common genetic changes underpinning cancer resistance in these long-lived species is yet to be fully established. Here, we newly generated a high-quality chromosome-level Asian elephant (Elephas maximus) genome and identified that the expanded gene families in elephants are involved in Ras-associated and base excision repair pathways. Moreover, we performed comparative genomic analyses of 12 mammals and examined genes with signatures of positive selection in elephants, naked mole rat, and greater horseshoe bat. Residues at positively selected sites of CDR2L and ALDH6A1 in these long-lived mammals enhanced the inhibition of tumor cell migration compared to those in short-lived relatives. Overall, our study provides a new genome resource and a preliminary survey of common genetic changes in long-lived mammals.
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Affiliation(s)
- Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pengcheng Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qi Pan
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Olatunde Omotoso
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yun Huang
- Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyBeijingChina
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27
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Mak L, Meleshko D, Danko DC, Barakzai WN, Maharjan S, Belchikov N, Hajirasouliha I. Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biol 2023; 24:197. [PMID: 37641111 PMCID: PMC10463629 DOI: 10.1186/s13059-023-03033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
Synthetic long read sequencing techniques such as UST's TELL-Seq and Loop Genomics' LoopSeq combine 3[Formula: see text] barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3[Formula: see text] unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.
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Affiliation(s)
- Lauren Mak
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - Dmitry Meleshko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - David C. Danko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | | | - Salil Maharjan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - Natan Belchikov
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine of Cornell University, New York, USA
| | - Iman Hajirasouliha
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
- Englander Institute for Precision Medicine, The Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, USA
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28
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Li H, Durbin R. Genome assembly in the telomere-to-telomere era. ARXIV 2023:arXiv:2308.07877v1. [PMID: 37645045 PMCID: PMC10462168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best but technological advances in long-read sequencing now enable near complete chromosome-level assembly, also known as telomere-to-telomere assembly, for many organisms. Here we review recent progress on assembly algorithms and protocols. We focus on how to derive near telomere-to-telomere assemblies and discuss potential future developments.
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Affiliation(s)
- Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Richard Durbin
- Department of Genetics, Cambridge University, Cambridge, UK
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Liang TS, Tang N, Xian MH, Wen WL, Huang CJ, Cai LH, Li QL, Wu YH. Identification of Critical Biomarkers and Mechanisms of Fructus Ligustri Lucidi on Vitiligo Using Integrated Bioinformatics Analysis. Clin Cosmet Investig Dermatol 2023; 16:2061-2071. [PMID: 37575147 PMCID: PMC10416786 DOI: 10.2147/ccid.s413733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Objective Vitiligo is an autoimmune disease of the skin that targets pigment-producing melanocytes and results in patches of depigmentation that are visible as white spots. Recent research studies have yielded a strong mechanistic understanding of this disease. Fructus Ligustri Lucidi (FLL) has been used for premature graying of hair since ancient China and is currently used to treat vitiligo. However, the key biomarkers and mechanisms underlying FLL in vitiligo remain unclear. This study aimed to identify the potential biomarkers and mechanisms of FLL in vitiligo using network pharmacology analysis. Methods The expression profiles of GSE65127 and GSE75819 were downloaded from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) between the vitiligo and healthy samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs were performed using R analyses. We performed R to further understand the functions of the critical targets. Cytoscape tools have facilitated network topology analysis. Molecular docking was performed using Auto Dock Vina software. Results The results showed that 13 DEGs were screened in vitiligo. Based on bioinformatics, network pharmacology and Western blot, we found that the critical targets of melanoma antigen recognized by 5,6-dihydroxyindole-2-carboxylic acid oxidase (TYRP1) may be related to the mechanism of action of FLL in the treatment of vitiligo. Conclusion TYRP1, as a melanocyte molecular biomarker, may be closely related to the underlying mechanism of FLL in the treatment of vitiligo via the inhibition of melanocyte death.
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Affiliation(s)
- Tian-Shan Liang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Nan Tang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Ming-Hua Xian
- School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Wei-Lun Wen
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Chang-Jin Huang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Lan-Hua Cai
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Qi-Lin Li
- Department of Dermatology, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
| | - Yan-Hua Wu
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, Guangdong, 510220, People’s Republic of China
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Sahu SK, Liu M, Chen Y, Gui J, Fang D, Chen X, Yang T, He C, Cheng L, Yang J, Sahu DN, Li L, Wang H, Mu W, Wei J, Liu J, Zhao Y, Zhang S, Lisby M, Liu X, Xu X, Li L, Wang S, Liu H. Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis). Sci Data 2023; 10:512. [PMID: 37537171 PMCID: PMC10400565 DOI: 10.1038/s41597-023-02420-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.
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Affiliation(s)
- Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinshan Gui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 311300, Hangzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xiaoli Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Chengzhong He
- Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Le Cheng
- BGI Research, Kunming, Yunnan, 650106, China
| | - Jinlong Yang
- BGI Research, Kunming, Yunnan, 650106, China
- College of Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Durgesh Nandini Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili, 678600, China
| | | | - Shouzhou Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150400, China.
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Ahsan MU, Liu Q, Perdomo JE, Fang L, Wang K. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nat Methods 2023; 20:1143-1158. [PMID: 37386186 DOI: 10.1038/s41592-023-01932-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of structural variants (SVs) from long reads. Long reads enable detection of SVs that could not be previously detected from short-read sequencing, but computational methods must adapt to the unique challenges and opportunities presented by long-read sequencing. Here, we summarize over 50 long-read-based methods for SV detection, genotyping and visualization, and discuss how new telomere-to-telomere genome assemblies and pangenome efforts can improve the accuracy and drive the development of SV callers in the future.
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Affiliation(s)
- Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan Elliot Perdomo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Zwaig M, Johnston MJ, Lee JJ, Farooq H, Gallo M, Jabado N, Taylor MD, Ragoussis J. Linked-read based analysis of the medulloblastoma genome. Front Oncol 2023; 13:1221611. [PMID: 37576901 PMCID: PMC10419201 DOI: 10.3389/fonc.2023.1221611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Medulloblastoma is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases. However, the molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants in recurrently affected genes typically requires the application of long-read technologies. Methods Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements. Results We demonstrate the detection of complex structural variants and point mutations in these tumors, and, for the first time, the detection of extrachromosomal DNA (ecDNA) with linked-reads. We provide further evidence for the high heterogeneity of somatic mutations in G4 MBs and add new complex events associated with it. Discussion We detected several enhancer-hijacking events, an ecDNA containing the MYCN gene, and rare structural rearrangements, such a chromothripsis in a G4 medulloblastoma, chromoplexy involving 8 different chromosomes, a TERT gene rearrangement, and a PRDM6 duplication.
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Affiliation(s)
- Melissa Zwaig
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael J. Johnston
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John J.Y. Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States
| | | | - Marco Gallo
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children’s Cancer Center , Hematology-Oncology Section and Department of Pediatrics – Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, United States
| | - Jiannis Ragoussis
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Liu B, Cui L, Deng Z, Ma Y, Yang D, Gong Y, Xu Y, Lan T, Yang S, Huang S. The genome assembly and annotation of the many-banded krait, Bungarus multicinctus. GIGABYTE 2023; 2023:gigabyte82. [PMID: 37404266 PMCID: PMC10315667 DOI: 10.46471/gigabyte.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Snakes are a vital component of wildlife resources and are widely distributed across the globe. The many-banded krait Bungarus multicinctus is a highly venomous snake found across Southern Asia and central and southern China. Snakes are an ancient reptile group, and their genomes can provide important clues for understanding the evolutionary history of reptiles. Additionally, genomic resources play a crucial role in comprehending the evolution of all species. However, snake genomic resources are still scarce. Here, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides genomic information on the genes involved in venom gland functions.
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Affiliation(s)
- Boyang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Liangyu Cui
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Zhangwen Deng
- Guangxi Forest Inventory and Planning Institute, Nanning 530011, China
| | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Diancheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
| | - Yanan Gong
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Huangshan Noah Biodiversity Institute, Huangshan 245000, China
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Zhao Y, Chen D, Chen K, Xie M, Guo J, Chan EWC, Xie L, Wang J, Chen E, Chen S, Chen W, Jelsbak L. Epidemiological and Genetic Characteristics of Clinical Carbapenem-Resistant Pseudomonas aeruginosa Strains in Guangdong Province, China. Microbiol Spectr 2023; 11:e0426122. [PMID: 37078855 PMCID: PMC10269565 DOI: 10.1128/spectrum.04261-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a bacterial pathogen that may cause serious drug-resistant infections that are potentially fatal. To investigate the genetic characteristics of these organisms, we tested 416 P. aeruginosa strains recovered from 12 types of clinical samples collected in 29 different hospital wards in 10 hospitals in Guangdong Province, China, from 2017 to 2020. These strains were found to belong to 149 known sequence types (STs) and 72 novel STs, indicating that transmission of these strains involved multiple routes. A high rate of resistance to imipenem (89.4%) and meropenem (79.4%) and a high prevalence of pathogenic serotypes (76.4%) were observed among these strains. Six STs of global high-risk clones (HiRiCs) and a novel HiRiC strains, ST1971, which exhibited extensive drug resistance, were identified. Importantly, ST1971 HiRiC, which was unique in China, also exhibited high virulence, which alarmed the further surveillance on this highly virulent and highly resistant clone. Inactivation of the oprD gene and overexpression of efflux systems were found to be mainly responsible for carbapenem resistance in these strains; carriage of metallo-β-lactamase (MBL)-encoding genes was less common. Interestingly, frameshift mutations (49.0%) and introduction of a stop codon (22.4%) into the oprD genes were the major mechanisms of imipenem resistance. On the other hand, expression of the MexAB-OprM efflux pump and MBL-encoding genes were mechanisms of resistance in >70% of meropenem-resistant strains. The findings presented here provide insights into the development of effective strategies for control of worldwide dissemination of CRPA. IMPORTANCE Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a major concern in clinical settings worldwide, yet few genetic and epidemiological studies on CRPA strains have been performed in China. Here, we sequence and analyze the genomes of 416 P. aeruginosa strains from hospitals in China to elucidate the genetic, phenotypic, and transmission characteristics of CRPA strains and to identify the molecular signatures responsible for the observed increase in the prevalence of CRPA infections in China. These findings may provide new insight into the development of effective strategies for worldwide control of CRPA and minimize the occurrence of untreatable infections in clinical settings.
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Affiliation(s)
- Yonggang Zhao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, People’s Republic of China
| | - Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, People’s Republic of China
| | - Jiubiao Guo
- College of Pharmacy-Shenzhen Technology University, Shenzhen, People’s Republic of China
| | - Edward Wai Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, People’s Republic of China
| | - Lu Xie
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, People’s Republic of China
| | - Jingbo Wang
- College of Pharmacy-Shenzhen Technology University, Shenzhen, People’s Republic of China
| | - Enqi Chen
- College of Pharmacy-Shenzhen Technology University, Shenzhen, People’s Republic of China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, People’s Republic of China
| | - Weijun Chen
- BGI-Shenzhen, Shenzhen, People’s Republic of China
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Jiang R, Yang M, Zhang S, Huang M. Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Comput Struct Biotechnol J 2023; 21:3073-3080. [PMID: 37273851 PMCID: PMC10238454 DOI: 10.1016/j.csbj.2023.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that originate from genomic DNA but are separate from chromosomes. They are common in various organisms, with sizes ranging from a few hundred to millions of base pairs. A special type of large extrachromosomal DNA (ecDNA) is prevalent in cancer cells. Research on ecDNA has significantly contributed to our comprehension of cancer development, progression, evolution, and drug resistance. The use of next-generation (NGS) and third-generation sequencing (TGS) techniques to identify eccDNAs throughout the genome has become a trend in current research. Here, we briefly review current advances in the biological mechanisms and applications of two distinct types of eccDNAs: microDNA and ecDNA. In addition to presenting available identification tools based on sequencing data, we summarize the most recent efforts to integrate ecDNA with single-cell analysis and put forth suggestions to promote the process.
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Fang C, Sun X, Fan F, Zhang X, Wang O, Zheng H, Peng Z, Luo X, Chen A, Zhang W, Drmanac R, Peters BA, Song Z, Kristiansen K. High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities. CELL REPORTS METHODS 2023; 3:100437. [PMID: 37056375 PMCID: PMC10088238 DOI: 10.1016/j.crmeth.2023.100437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
Sequencing of hypervariable regions as well as internal transcribed spacer regions of ribosomal RNA genes (rDNA) is broadly used to identify bacteria and fungi, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length using high throughput, cost-efficient second-generation sequencing. We developed a method to obtain nearly full-length rDNA by assembling single DNA molecules combining DNA co-barcoding with single-tube long fragment read technology and second-generation sequencing. Benchmarking was performed using mock bacterial and fungal communities as well as two forest soil samples. All mock species rDNA were successfully recovered with identities above 99.5% compared to the reference sequences. From the soil samples we obtained good coverage with identification of more than 20,000 unknown species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.
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Affiliation(s)
- Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Fei Fan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Ou Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China
- Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhuobing Peng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Radoje Drmanac
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Brock A. Peters
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450 Copenhagen, Denmark
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531179. [PMID: 36945366 PMCID: PMC10028795 DOI: 10.1101/2023.03.05.531179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked-that is, phased-is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as 'linked-reads'). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Peter L. Chang
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093 USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
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Weisweiler M, Stich B. Benchmarking of structural variant detection in the tetraploid potato genome using linked-read sequencing. Genomics 2023; 115:110568. [PMID: 36702293 DOI: 10.1016/j.ygeno.2023.110568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]
Abstract
It has recently been shown that structural variants (SV) can have a higher impact on gene expression variation compared to single nucleotide variants (SNV) in different plant species. Additionally, SV were associated with phenotypic variation in several crops. However, compared to the established SV detection based on short-read sequencing, less approaches were described for linked-read based SV calling. We therefore evaluated the performance of six linked-read SV callers compared to an established short-read SV caller based on simulated linked-reads in tetraploid potato. The objectives of our study were to i) compare the performance of SV callers based on linked-read sequencing to short-read sequencing, ii) examine the influence of SV type, SV length, haplotype incidence (HI), as well as sequencing coverage on the SV calling performance in the tetraploid potato genome, and iii) evaluate the accuracy of detecting insertions by linked-read compared to short-read sequencing. We observed high break point resolutions (BPR) detecting short SV and slightly lower BPR for large SV. Our observations highlighted the importance of short-read signals provided by Manta and LinkedSV to detect short SV. Manta and NAIBR performed well for detecting larger deletions, inversions, and duplications. Detected large SV were weakly influenced by the HI. Furthermore, we illustrated that large insertions can be assembled by Novel-X. Our results suggest the usage of the short-read and linked-read SV callers Manta, NAIBR, LinkedSV, and Novel-X based on at least 90x linked-read sequencing coverage to ensure the detection of a broad range of SV in the tetraploid potato genome.
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Affiliation(s)
- Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Universitätsstraße 1, 40225 Düsseldorf, Germany; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany.
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40
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Tian S, Wu L, Zheng H, Zhong X, Yu X, Wu W. Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis. Hereditas 2023; 160:8. [PMID: 36855217 PMCID: PMC9976393 DOI: 10.1186/s41065-023-00269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Neuropathic pain (NP) is one of the most common types of chronic pain and significantly compromises the quality of life. Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis in response to various stresses. The role of autophagy-related genes in the diagnosis and treatment of neuropathic pain remains unclear. METHODS We identified autophagy-related differentially expressed genes (ARDEGs) and differentially expressed miRNAs (DE-miRNAs) in neuropathic pain by bioinformatics analysis of the GSE145226 and GSE145199 datasets. These ARDEGs and their co-expressed genes were subjected to Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and friends analysis. Meanwhile, we constructed TFs-ARDEGs, miRNA-ARDEGs regulatory network through ChIPBase database and the HTFtarget database, multiMir R package. Finally, we performed immune infiltration analysis of ARDEGs by Single Sample Gene Set Enrichment Analysis (ssGSEA). RESULTS We identified 2 potential autophagy-related differentially expressed genes (Sirt2 and ST7) that may be closely associated with the pathogenesis of neuropathic pain. GO, KEGG and GSEA analysis revealed that these two ARDEGs were mainly enriched in pyridine nucleotide metabolic process, nicotinamide nucleotide metabolic process, Nicotinate and nicotinamide metabolism, NF-κB pathway, KRAS signaling, P53 pathway. In the TFs-ARDEGs and miRNA-ARDEGs regulatory network, miR-140-5p and Cebpb were predicted to be as crucial regulators in the progression of NP. For the ssGSEA results, Sirt2 was positively correlated with Eosinophil and Effector memory CD8+ T cell infiltration, which suggested that it may be involved in the regulation of neuroimmune-related signaling. CONCLUSION Two autophagy-related differentially expressed genes, especially Sirt2, may be potential biomarkers for NP, providing more evidence about the crucial role of autophagy in neuropathic pain.
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Affiliation(s)
- Sheng Tian
- grid.412455.30000 0004 1756 5980Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006 China
| | - Lanxiang Wu
- grid.412455.30000 0004 1756 5980Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006 China
| | - Heqing Zheng
- grid.412455.30000 0004 1756 5980Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006 China
| | - Xianhui Zhong
- grid.412455.30000 0004 1756 5980Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006 China
| | - Xinping Yu
- grid.412455.30000 0004 1756 5980Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006 China
| | - Wei Wu
- Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
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41
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Kang H, Liu Q, Seim I, Zhang W, Li H, Gao H, Lin W, Lin M, Zhang P, Zhang Y, Gao H, Wang Y, Qin Y, Liu M, Dong L, Yang Z, Zhang Y, Han L, Fan G, Li S. A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour 2023. [PMID: 36826393 DOI: 10.1111/1755-0998.13775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.
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Affiliation(s)
- Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, Qingdao, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenwei Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Haiyu Gao
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | - Yang Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yating Qin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Mingming Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Lei Han
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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42
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Nguyen TV, Vander Jagt CJ, Wang J, Daetwyler HD, Xiang R, Goddard ME, Nguyen LT, Ross EM, Hayes BJ, Chamberlain AJ, MacLeod IM. In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genet Sel Evol 2023; 55:9. [PMID: 36721111 PMCID: PMC9887926 DOI: 10.1186/s12711-023-00783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (< 50 bp), it has been challenging to accurately identify and genotype SV at the population scale using short-read sequencing. Long-read sequencing technologies are becoming competitively priced and can address several of the disadvantages of short-read sequencing for the discovery and genotyping of SV. In livestock species, analysis of SV at the population scale still faces challenges due to the lack of resources, high costs, technological barriers, and computational limitations. In this review, we summarize recent progress in the characterization of SV in the major livestock species, the obstacles that still need to be overcome, as well as the future directions in this growing field. It seems timely that research communities pool resources to build global population-scale long-read sequencing consortiums for the major livestock species for which the application of genomic tools has become cost-effective.
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Affiliation(s)
- Tuan V. Nguyen
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Christy J. Vander Jagt
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Jianghui Wang
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Hans D. Daetwyler
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia ,grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
| | - Ruidong Xiang
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia ,grid.1008.90000 0001 2179 088XFaculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Michael E. Goddard
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia ,grid.1008.90000 0001 2179 088XFaculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Loan T. Nguyen
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Elizabeth M. Ross
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Ben J. Hayes
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072 Australia
| | - Amanda J. Chamberlain
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia ,grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
| | - Iona M. MacLeod
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
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43
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Liu Y, Fan F, Drmanac R, Peters BA, Wang O. Large-Scale Complete Sequencing and Haplotyping of 1-10 kb DNA Molecules Using Short Massively Parallel Reads. Methods Mol Biol 2023; 2590:59-70. [PMID: 36335492 DOI: 10.1007/978-1-0716-2819-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we describe a simple, low-cost method for making many copies of a single DNA molecule (1-10 kb in length) as a concatemer on a long DNA strand. This can enable applications requiring high-quality contiguous sequence and haplotype data from long single DNA molecules at large scale.
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Affiliation(s)
- Youtao Liu
- MGI, Shenzhen, Guangdong Province, PR China
| | - Fei Fan
- BGI-Shenzhen, Shenzhen, Guangdong Province, PR China
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA
| | - Ou Wang
- BGI-Shenzhen, Shenzhen, Guangdong Province, PR China.
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44
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Wang O, Cheng X, Drmanac R, Peters BA. A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly. Methods Mol Biol 2023; 2590:101-125. [PMID: 36335495 DOI: 10.1007/978-1-0716-2819-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we describe single-tube long fragment read (stLFR), a simple preparation method for whole-genome sequencing and physical haplotyping based on the DNA co-barcoding strategy. Similar to LFR, stLFR applies the concept of adding the same barcode to subfragments derived from the same long DNA molecule. However, instead of a 384-well plate, stLFR uses the surface of micron-sized magnetic beads to create millions of virtual compartments in a single reaction tube. This is enabled by a split and pool barcoded bead preparation process capable of generating ~500,000 copies of the same unique barcode, from a library of ~3.6 billion unique barcodes, on each bead. The instruments and devices used in the stLFR process are easily accessible in nearly all standard molecular biology laboratories, and the cost of reagents can be as low as 30 dollars per sample. stLFR libraries can be sequenced by standard second-generation sequencing instruments (e.g., MGI or Illumina devices), and the barcode sharing information enables detection and phasing of all variations, including large structural variations. In addition, stLFR data can be used to scaffold contigs and de novo assemble genomes.
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Affiliation(s)
- Ou Wang
- BGI-Shenzhen, Shenzhen, Guangdong Province, People's Republic of China
| | - Xiaofang Cheng
- MGI, Shenzhen, Guangdong Province, People's Republic of China
| | - Radoje Drmanac
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA
| | - Brock A Peters
- Advanced Genomics Technology Laboratory, Complete Genomics/MGI, San Jose, CA, USA.
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45
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Duitama J. Phased Genome Assemblies. Methods Mol Biol 2023; 2590:273-286. [PMID: 36335504 DOI: 10.1007/978-1-0716-2819-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The ultimate goal of de novo assembly of reads sequenced from a diploid individual is the separate reconstruction of the sequences corresponding to the two copies of each chromosome. Unfortunately, the allele linkage information needed to perform phased genome assemblies has been difficult to generate. Hence, most current genome assemblies are a haploid mixture of the two underlying chromosome copies present in the sequenced individual. Sequencing technologies providing long (20 kb) and accurate reads are the basis to generate phased genome assemblies. This chapter provides a brief overview of the main milestones in traditional genome assembly, focusing on the bioinformatic techniques developed to generate haplotype information from different specialized protocols. Using these techniques as a knowledge background, the chapter reviews the current algorithms to generate phased assemblies from long reads with low error rates. Current techniques perform haplotype-aware error correction steps to increase the quality of the raw reads. In addition, variations on the traditional overlap-layout-consensus (OLC) graph have been developed in an effort to eliminate edges between reads sequenced from different chromosome copies. This allows for large presence-absence variants between the chromosome copies to be taken into account. The development of these algorithms, along with the improved sequencing technologies has been crucial to finish chromosome-level assemblies of complex genomes.
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Affiliation(s)
- Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
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46
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Zhao Y, Chen D, Ji B, Zhang X, Anbo M, Jelsbak L. Whole-genome sequencing reveals high-risk clones of Pseudomonas aeruginosa in Guangdong, China. Front Microbiol 2023; 14:1117017. [PMID: 37125174 PMCID: PMC10140354 DOI: 10.3389/fmicb.2023.1117017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
The ever-increasing prevalence of infections produced by multidrug-resistant or extensively drug-resistant Pseudomonas aeruginosa is commonly linked to a limited number of aptly-named epidemical 'high-risk clones' that are widespread among and within hospitals worldwide. The emergence of new potential high-risk clone strains in hospitals highlights the need to better and further understand the underlying genetic mechanisms for their emergence and success. P. aeruginosa related high-risk clones have been sporadically found in China, their genome sequences have rarely been described. Therefore, the large-scale sequencing of multidrug-resistance high-risk clone strains will help us to understand the emergence and transmission of antibiotic resistances in P. aeruginosa high-risk clones. In this study, 212 P. aeruginosa strains were isolated from 2 tertiary hospitals within 3 years (2018-2020) in Guangdong Province, China. Whole-genome sequencing, multi-locus sequence typing (MLST) and antimicrobial susceptibility testing were applied to analyze the genomic epidemiology of P. aeruginosa in this region. We found that up to 130 (61.32%) of the isolates were shown to be multidrug resistant, and 196 (92.45%) isolates were Carbapenem-Resistant Pseudomonas aeruginosa. MLST analysis demonstrated high diversity of sequence types, and 18 reported international high-risk clones were identified. Furthermore, we discovered the co-presence of exoU and exoS genes in 5 collected strains. This study enhances insight into the regional research of molecular epidemiology and antimicrobial resistance of P. aeruginosa in China. The high diversity of clone types and regional genome characteristics can serve as a theoretical reference for public health policies and help guide measures for the prevention and control of P. aeruginosa resistance.
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Affiliation(s)
- Yonggang Zhao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dingqiang Chen
- Department of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Mikkel Anbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Lars Jelsbak,
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47
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Cui Y, Cao M. Liquid Biopsy in Bladder Cancer. Methods Mol Biol 2023; 2695:111-120. [PMID: 37450114 DOI: 10.1007/978-1-0716-3346-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Fluid biopsy based on circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosome, and circulating RNA in blood and body fluids has gained attention. Here, the recent findings and issues related to liquid biopsy in bladder cancer are discussed, with a focus on CTCs, ctDNA, urinary tumor DNA, exosome, and circulating RNA.
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Affiliation(s)
- Yan Cui
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, People's Republic of China
| | - Muyang Cao
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, People's Republic of China
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48
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Hu Y, Yang C, Zhang L, Zhou X. Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads. Methods Mol Biol 2023; 2590:161-182. [PMID: 36335499 DOI: 10.1007/978-1-0716-2819-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phasing is essential for determining the origins of each set of alleles in the whole-genome sequencing data of individuals. As such, it provides essential information for the causes of hereditary diseases and the sources of individual variability. Recent technical breakthroughs in linked-read (referred to as co-barcoding in other chapters of the book) and long-read sequencing and downstream analysis have brought the goal of accurate and complete phasing within reach. Here we review recent progress related to the assembly and phasing of personal genomes based on linked-reads and related applications. Motivated by current limitations in generating high-quality diploid assemblies and detecting variants, a new suite of software tools, Aquila, was developed to fully take advantage of linked-read sequencing technology. The overarching goal of Aquila is to exploit the strengths of linked-read technology including long-range connectivity and inherent phasing of variants for reference-assisted local de novo assembly at the whole-genome scale. The diploid nature of the assemblies facilitates detection and phasing of genetic variation, including single nucleotide variations (SNVs), small insertions and deletions (indels), and structural variants (SVs). An extension of Aquila, Aquila_stLFR, focuses on another newly developed linked-reads sequencing technology, single-tube long-fragment read (stLFR). AquilaSV, a region-based diploid assembly approach, is used to characterize structural variants and can achieve diploid assembly in one target region at a time. Lastly, we introduce HAPDeNovo, a program that exploits phasing information from linked-read sequencing to improve detection of de novo mutations. Use of these tools is expected to harness the advantages of linked-reads technology, improve phasing, and advance variant discovery.
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Affiliation(s)
- Yunfei Hu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Xin Zhou
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
- Data Science Institute, Nashville, TN, USA.
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Huang Y, Jiang P, Liang Z, Chen R, Yue Z, Xie X, Guan C, Fang X. Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing. Front Microbiol 2023; 14:1145315. [PMID: 37213501 PMCID: PMC10196144 DOI: 10.3389/fmicb.2023.1145315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.
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Affiliation(s)
- Yufen Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya, China
| | | | - Changge Guan
- BGI-Sanya, BGI-Shenzhen, Sanya, China
- *Correspondence: Changge Guan
| | - Xiaodong Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Xiaodong Fang
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Adam E, Ranjan D, Riethman H. NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads. BMC Bioinformatics 2022; 23:545. [PMID: 36526983 PMCID: PMC9758922 DOI: 10.1186/s12859-022-05081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function. RESULTS We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with mapped ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets of DNA sequences identified by matches with 1-copy subtelomere sequence adjacent to segmental duplications are assembled and extended into the segmental duplication regions using Regional Extension of Assemblies using Linked-Reads (REXTAL). Mapped telomere-containing ultralong nanopore reads are then used to provide contiguity and correct orientation for matching REXTAL sequence contigs as well as identification/correction of any misassemblies. Our method was tested for a subset of representative subtelomeres with ultralong nanopore read coverage in the haploid human cell line CHM13. A 10X Linked-Read dataset from CHM13 was combined with ultralong nanopore reads from the same genome to provide improved subtelomere assemblies. Comparison of Nanopore-only assemblies using SHASTA with our NPGREAT assemblies in the distal-most subtelomere regions showed that NPGREAT produced higher-quality and more complete assemblies than SHASTA alone when these regions had low ultralong nanopore coverage (such as cases where large segmental duplications were immediately adjacent to (TTAGGG) tracts). CONCLUSION In genomic regions with large segmental duplications adjacent to telomeres, NPGREAT offers an alternative economical approach to improving assembly accuracy and coverage using linked-read datasets when more expensive HiFi datasets of 10-20 kb reads are unavailable.
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Affiliation(s)
- Eleni Adam
- grid.261368.80000 0001 2164 3177Department of Computer Science, Old Dominion University, Norfolk, VA USA
| | - Desh Ranjan
- grid.261368.80000 0001 2164 3177Department of Computer Science, Old Dominion University, Norfolk, VA USA
| | - Harold Riethman
- grid.261368.80000 0001 2164 3177Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA USA
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