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From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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Marine Life Science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu Xue Zhang Yunyi Gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng Gao Key Laboratory of Evolution&Marine Biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of Biology Bradley UniversityPeoriaIL 61625USA Laoshan Laboratory Qingdao 266237China

genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic ***,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of *** expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline *** in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic *** report the partial germline genomes of two spirotrich ciliate species,namely Strombidium *** and Halteria grandinella,along with the most compact and highly fragmented somatic genome for *** provide the first insights into the genome rearrangements of these two species and compare these features with those of other *** analyses reveal:(1)DNA sequence loss through evolution and during PGR in *** has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing Ciliates Gene scrambling genome rearrangement Germline genome Somatic genome

Chromosome rearrangement revealed by comparison of willow high density genetic map and poplar genome sequence

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Chromosome rearrangement revealed by comparison of willow hi...

Sorting Unsigned Permutations by Weighted Reversals,Transpositions,and Transreversals

遗传学与表观遗传学前沿暨第三届中国青年遗传学家论坛

作者： Defang Zhang Tao Xia Kai Feng Jing Hou Tongming Yin Key Lab of Forest Genetics and biotechnology Nanjing Forestry University

Willows(Salix)and poplars(Populus)are members of the Salicaceae *** originated from the same ancestor and share many biological *** the increasing interest in using willow for biomass production,great pressure was exerted in high-yielding *** view of their important role in economy,phylogeny and some other aspect,and to successfully transfer genetic information from poplar to willow,an appreciation of their genome difference and the chromosome structural evolution is necessary.A high density genetic map of willow was constructed with 6,901 SNP markers based on next generation sequencing *** aligning this high density map to the publicly available poplar genome sequence,two major chromosomal rearrangements were found,involving LG1and LG6 in willow,LGI and LGXVI in poplar,these data support a fission and a fusion event between poplar and willow *** addition,eight significant inversions were identified,involving LG2,LG0,LG3,LG5 and LG9 in *** observed two major chromosome rearrangement events suggest that poplar and willow may have three different repattering types in the processing of chromosomal reconstruction after whole genome duplication,and these different repattering types may contributed to the divergence between poplar and willow.A large inversion involving LG9 in willow and LGXIX in poplar may relate to the difference of sex determination loci between willow and poplar.

关键词： genome rearrangement Willow Poplar Genetic map NGS

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Journal of Computer Science & Technology 2010年第4期25卷 853-863页

作者：娄晓文朱大铭 School of Computer Science and Technology Shandong University

Reversals, transpositions and transreversals are common events in genome rearrangement. The genome rearrangement sorting problem is to transform one genome into another using the minimum number of given rearrangement operations. An integer permutation is used to represent a genome in many cases. It can be divided into disjoint strips with each strip denoting a block of consecutive integers. A singleton is a strip of one integer. And the genome rearrange- ment problem turns into the problem of sorting a permutation into the identity permutation equivalently. Hannenhalli and Pevzner designed a polynomial time algorithm for the unsigned reversal sorting problem on those permutations with O（logn） singletons. In this paper, first we describe one case in which Hannenhalli and Pevzner＇s algorithm may fail and propose a corrected approach. In addition, we propose a （1 ＋ ε）-approximation algorithm for sorting unsigned permutations with O（log n） singletons by reversals of weight 1 and transpositions/transreversals of weight 2.

关键词： approximation algorithm genome rearrangement sorting reversal transposition

维普期刊数据库

Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

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National Science Review 2023年第5期10卷 240-250页

作者： Sijie Zhou Yi Wu Yu Zhao Zhen Zhang Limin Jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan Frontiers Science Center for Synthetic Biology (Ministry of Education) Tianjin University Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin University Institute for Systems Genetics NYU Langone Health School of Computer Science and Technology College of Intelligence and ComputingTianjin University Epigenetic Group Frasergen Bioinformatics Co.Ltd. Department of Computer Science University of South Carolina

Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary *** Chromosome rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural ***,we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of *** further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact *** rearrangements tend to occur in 3D spatially proximal and chromatin-accessible *** enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关键词： synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRaMbLE Saccharomyces cerevisiae

A New Approximation Algorithm for Sorting of Signed Permutations

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Journal of Computer Science & Technology 2003年第1期18卷 125-130页

作者：何勇陈汀 DepartmentofMathematics ZheiangUniversityHangzhou310027P.R.China

Sequence comparison leads to a combinatorial optimization problem of sorting permutations by reversals and transpositions. Namely, given any two permutations, find the shortest distance between them. This problem is related with genome rearrangement. The sorting of signed permutations is studied. Because in genome rearrangement, genes are oriented in DNA sequences. The transpositions which have been studied in the literature can be viewed as operations working on two consecutive segments of the genome. In this paper, a new kind of transposition which can work on two arbitrary segments of the genome is proposed, and the sorting of signed permutations by reversals and this new kind of transpositions are studied. After establishing a lower bound on the number of operations needed, a 2-approximation algorithm is presented for this problem and an example is given to show that the performance ratio of the algorithm cannot be improved.

关键词： sorting of permutation genome rearrangement approximation algorithm

Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles

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Frontiers of Chemical Science and Engineering 2018年第4期12卷 806-814页

作者： Juan Wang Bin Jia Zexiong Xie Yunxiang Li Yingjin Yuan Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin UniversityTianjin 300072China SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)Tianjin University Tianjin 300072China

The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system has been used to improve prodeoxyviolacein (PDV) production in haploid yeast containing chromosome synV. To rapidly and continuously generate genome diversification with the desired phenotype, the multiplex SCRaMbLE iterative cycle strategy has been developed for the screening of high PDV production strains. Whole-genome sequencing analysis reveals large duplications, deletions, and even the whole genome duplications. The deletion of YER151C is proved to be responsible for the increase. This study demonstrates that artificial DNA rearrangement can be used to accelerate microbial evolution and the production of biobased chemicals.

关键词： synthetic biology genome rearrangement prodeoxyviolacein SCRaMbLE Saccharomyces cerevisiae

Plastid genome sequencing,comparative genomics,and phylogenomics:Current status and prospects

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Journal of Systematics and Evolution 2010年第2期48卷 77-93页

作者： 1Lei GAO 2Ying-Juan SU 1Ting WANG 1(Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture,Wuhan Botanical Garden,Chinese Academy of Sciences,Wuhan 430074,China) 2(State Key Laboratory of Biocontrol,School of Life Sciences,Sun Yat-sen University,Guangzhou 510275,China) (Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan 430074 China) (State Key Laboratory of Biocontrol School of Life Sciences Sun Yat-sen University Guangzhou 510275 China)

More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing *** on this unprecedented abundance of data,extensive genomic changes have been revealed in the plastid *** is the most common mechanism that leads to gene order *** inversion events have been recognized as informative phylogenetic markers,such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all *** loss is a common event throughout plastid genome *** genes were independently lost or transferred to the nuclear genome in multiple plant *** trnR-CCG gene was lost in some clades of lycophytes,ferns,and seed plants,and all the ndh genes were absent in parasitic plants,gnetophytes,Pinaceae,and the Taiwan moth *** parasitic plants have,in particular,lost plastid genes related to photosynthesis because of the relaxation of functional *** dramatic growth of plastid genome sequences has also promoted the use of whole plastid sequences and genomic features to solve phylogenetic *** phylogenomics has provided additional evidence for deep-level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic ***,chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed.

关键词： chloroplast phylogenomics comparative genomics gene loss genome rearrangement plastid genome sequencing

Some Algorithmic Challenges in genome-Wide Ortholog Assignment

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Journal of Computer Science & Technology 2010年第1期25卷 42-52页

作者：姜涛 Department of Computer Science and Engineering University of California School of Information Science and Technology Tsinghua University

genome-scale assignment of orthologous genes is a fundamental and challenging problem in computational biology and has a wide range of applications in comparative genomics, functional genomics, and systems biology. Many methods based on sequence similarity, phylogenetic analysis, chromosomal syntenic information, and genome rearrangement have been proposed in recent years for ortholog assignment. Although these methods produce results that largely agree with each other, their results may still contain significant differences. In this article, we consider the recently proposed parsimony approach for assigning orthologs between closely related genomes based on genome rearrangement, which essentially attempts to transform one genome into another by the smallest number of genome rearrangement events including reversal, translocation, fusion, and fission, as well as gene duplication events. We will highlight some of the challenging algorithmic problems that arise in the approach including （i） minimum common substring partition, （ii） signed reversal distance with duplicates, and （iii） signed transposition distance with duplicates. The most recent progress towards the solution of these problems will be reviewed and some open questions will he posed. We will also discuss some possible extensions of the approach to the simultaneous comparison of multiple genomes.

关键词： algorithm comparative genomics computational biology genome rearrangement ortholog assignment

维普期刊数据库

The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing

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Asian Journal of Andrology 2013年第3期15卷 301-308页

作者： Alexander W Wyatt Fan Mo Yuzhuo Wang Colin C Collins Vancouver Prostate Centre & Department of Urologic Sciences University of British Columbia Vancouver BC V6H 3Z6 Canada Department of Experimental Therapeutics BC Cancer Agency Vancouver BC VSZ 1L3 Canada

Prostate cancer is a leading cause of global cancer-related death but attempts to improve diagnoses and develop novel therapies have been confounded by significant patient heterogeneity. In recent years, the application of next-generation sequencing to hundreds of prostate tumours has defined novel molecular subtypes and characterized extensive genomic aberration underlying disease initiation and progression. It is now clear that the heterogeneity observed in the clinic is underpinned by a molecular landscape rife with complexity, where genomic rearrangements and rare mutations combine to amplify transcriptomic diversity. This review dissects our current understanding of prostate cancer ＇omics＇, including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare. Therefore, it is critical that we continue to define individual tumour genomes, especially in the context of their expressed transcriptome. Only through improved characterisation of tumour to tumour variability can we advance to an age of precision therapy and personalized oncology.

关键词： cancer sequencing copy number fusion gene genome genome rearrangement personalized oncology prostate cancer transcriptome