断点图与祖先基因组重建
Breakpoint graphs and ancestral genome reconstructions.
作者信息
Alekseyev Max A, Pevzner Pavel A
机构信息
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0404, USA.
出版信息
Genome Res. 2009 May;19(5):943-57. doi: 10.1101/gr.082784.108. Epub 2009 Feb 13.
Abstract
Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.
摘要
最近完成的全基因组测序项目标志着从基于基因的系统发育研究向对整个基因组进行系统发育基因组学分析的转变。我们开发了一种用于重建祖先基因组的算法MGRA，并使用它来研究七个人类、黑猩猩、猕猴、小鼠、大鼠、狗和负鼠的哺乳动物基因组的重排历史。MGRA依靠多重断点图的概念来克服现有祖先基因组重建方法的一些局限性。当系统发育未知时，MGRA还会生成指导系统发育树重建的基于重排的特征。
相似文献
1
Breakpoint graphs and ancestral genome reconstructions.断点图与祖先基因组重建
Genome Res. 2009 May;19(5):943-57. doi: 10.1101/gr.082784.108. Epub 2009 Feb 13.
2
A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances.基于断点和重排距离对祖先基因组重建进行的统计学上公平的比较。
J Comput Biol. 2010 Sep;17(9):1299-314. doi: 10.1089/cmb.2010.0121.
3
Genome-scale evolution: reconstructing gene orders in the ancestral species.基因组规模的进化：重建祖先物种中的基因顺序。
Genome Res. 2002 Jan;12(1):26-36.
4
Colored de Bruijn graphs and the genome halving problem.彩色德布鲁因图与基因组减半问题。
IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):98-107. doi: 10.1109/TCBB.2007.1002.
5
Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.存在基因获得与丢失情况下的祖先基因组重建
J Comput Biol. 2016 Mar;23(3):150-64. doi: 10.1089/cmb.2015.0160. Epub 2016 Feb 17.
6
Reconstruction of ancestral gene orders using intermediate genomes.利用中间基因组重建祖先基因顺序
BMC Bioinformatics. 2015;16 Suppl 14(Suppl 14):S3. doi: 10.1186/1471-2105-16-S14-S3. Epub 2015 Oct 2.
7
Fast ancestral gene order reconstruction of genomes with unequal gene content.具有不等基因含量的基因组的快速祖先基因顺序重建
BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):413. doi: 10.1186/s12859-016-1261-9.
8
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions.一种用于解决带权重反转和转置的多基因组重排问题的快速算法。
BMC Bioinformatics. 2008 Dec 4;9:516. doi: 10.1186/1471-2105-9-516.
9
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.鸟类祖先染色体组型的重建揭示了巨染色体和微染色体进化历史的差异。
Genome Biol. 2018 Oct 5;19(1):155. doi: 10.1186/s13059-018-1544-8.
10
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes.重建原始哺乳动物的基因组结构：来自人类、小鼠和大鼠基因组的经验教训。
Genome Res. 2004 Apr;14(4):507-16. doi: 10.1101/gr.1975204.
引用本文的文献
1
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.西弗勒斯使用长读长测序技术检测癌症基因组中的体细胞结构变异和复杂重排。
Nat Biotechnol. 2025 Apr 4. doi: 10.1038/s41587-025-02618-8.
2
OMKar: optical map based automated karyotyping of genomes to identify constitutional abnormalities.OMKar：基于光学图谱的基因组自动核型分析，用于识别染色体结构异常。
medRxiv. 2025 Feb 14:2025.02.13.25322211. doi: 10.1101/2025.02.13.25322211.
3
GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.基因组解码器：推断高度重复基因组区域中的片段重复
Bioinformatics. 2025 Feb 4;41(2). doi: 10.1093/bioinformatics/btaf058.
4
Impact and characterization of serial structural variations across humans and great apes.人类和大型类人猿中连续结构变异的影响和特征。
Nat Commun. 2024 Sep 13;15(1):8007. doi: 10.1038/s41467-024-52027-9.
5
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.CoRAL 利用长读测序技术准确解析染色体外 DNA 基因组结构。
Genome Res. 2024 Oct 11;34(9):1344-1354. doi: 10.1101/gr.279131.124.
6
Genome Rearrangement Analysis : Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.基因组重排分析：切割和连接基因组重排及基因簇保护方法。
Methods Mol Biol. 2024;2802:215-245. doi: 10.1007/978-1-0716-3838-5_9.
7
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads.Severus：利用长读长技术对肿瘤基因组中的体细胞结构变异进行准确检测和特征分析。
medRxiv. 2024 Mar 26:2024.03.22.24304756. doi: 10.1101/2024.03.22.24304756.
8
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.CoRAL通过长读长测序准确解析染色体外DNA基因组结构。
bioRxiv. 2024 May 18:2024.02.15.580594. doi: 10.1101/2024.02.15.580594.
9
The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes.菜豆染色体水平基因组组装为食用胶（半乳甘露聚糖）生物合成家族基因提供了分子见解。
Sci Rep. 2023 Jun 19;13(1):9941. doi: 10.1038/s41598-023-33762-3.
10
KOMB: K-core based de novo characterization of copy number variation in microbiomes.KOMB：基于K核的微生物群落中拷贝数变异的从头表征。
Comput Struct Biotechnol J. 2022 Jun 17;20:3208-3222. doi: 10.1016/j.csbj.2022.06.019. eCollection 2022.
本文引用的文献
1
Recovering genome rearrangements in the mammalian phylogeny.在哺乳动物系统发育中恢复基因组重排
Genome Res. 2009 May;19(5):934-42. doi: 10.1101/gr.086009.108.
2
Multichromosomal median and halving problems under different genomic distances.不同基因组距离下的多染色体中位数和减半问题
BMC Bioinformatics. 2009 Apr 22;10:120. doi: 10.1186/1471-2105-10-120.
3
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.一种用于重建祖先基因组连续区域的方法框架及其在哺乳动物基因组中的应用。
PLoS Comput Biol. 2008 Nov;4(11):e1000234. doi: 10.1371/journal.pcbi.1000234. Epub 2008 Nov 28.
4
Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes.多断点重排与断点再利用：从环状基因组到线性基因组
J Comput Biol. 2008 Oct;15(8):1117-31. doi: 10.1089/cmb.2008.0080.
5
The infinite sites model of genome evolution.基因组进化的无限位点模型。
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14254-61. doi: 10.1073/pnas.0805217105. Epub 2008 Sep 11.
6
Estimating true evolutionary distances under the DCJ model.在DCJ模型下估计真实的进化距离。
Bioinformatics. 2008 Jul 1;24(13):i114-22. doi: 10.1093/bioinformatics/btn148.
7
Chromosomal phylogeny and evolution of the African mole-rats (Bathyergidae).非洲鼹形鼠（滨鼠科）的染色体系统发育与进化
Chromosome Res. 2008;16(1):57-74. doi: 10.1007/s10577-007-1200-8.
8
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.17号染色体上的类人猿染色体重排定位于节段性重复的复杂区域。
Genome Biol. 2008;9(2):R28. doi: 10.1186/gb-2008-9-2-r28. Epub 2008 Feb 7.
9
A recurrent inversion on the eutherian X chromosome.真兽类X染色体上的一个反复出现的倒位。
Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18571-6. doi: 10.1073/pnas.0706604104. Epub 2007 Nov 14.
10
Initial sequence and comparative analysis of the cat genome.猫基因组的初始序列及比较分析。
Genome Res. 2007 Nov;17(11):1675-89. doi: 10.1101/gr.6380007.
Zotero 插件