Abstract：
:Horizontal gene transfer (HGT) has been shown to widely spread in organisms by comparative genomic studies. However, its effect on the phylogenetic relationship of organisms, especially at a system level of different cellular functions, is still not well understood. In this work, we have constructed phylogenetic trees based on the enzyme, reaction, and gene contents of metabolic networks reconstructed from annotated genome information of 82 sequenced organisms. Results from different phylogenetic distance definitions and based on three different functional subsystems (i.e., metabolism, cellular processes, information storage and processing) were compared. Results based on the three different functional subsystems give different pictures on the phylogenetic relationship of organisms, reflecting the different extents of HGT in the different functional systems. In general, horizontal transfer is prevailing in genes for metabolism, but less in genes for information processing. Nevertheless, the major results of metabolic network-based phylogenetic trees are in good agreement with the tree based on 16S rRNA and genome trees, confirming the three domain classification and the close relationship between eukaryotes and archaea at the level of metabolic networks. These results strongly support the hypothesis that although HGT is widely distributed, it is nevertheless constrained by certain pre-existing metabolic organization principle(s) during the evolution. Further research is needed to identify the organization principle and constraints of metabolic network on HGT which have large impacts on understanding the evolution of life and in purposefully manipulating cellular metabolism.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Ma HW,Zeng APdoi
10.1016/j.ympev.2003.08.011keywords:
subject
Has Abstractpub_date
2004-04-01 00:00:00pages
204-13issue
1eissn
1055-7903issn
1095-9513pii
S1055790303003075journal_volume
31pub_type
杂志文章abstract：:MSP-7 is a surface protein expressed by the Plasmodium merozoite as part of a protein-complex involved in initial interaction between merozoite and erythrocyte. Contigs of seven Plasmodium species were analyzed in order to identify all msp-7 family genes. The search identified annotated and unannotated open reading fr...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
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更新日期：2010-05-01 00:00:00
abstract：:The habit of mining within leaves has evolved convergently in numerous plant-feeding insect taxa. Many leaf-mining groups contain a large number of species with distinct feeding preferences, which makes them highly suitable for studies on the evolutionary history of host-plant use and on the role of niche shifts in sp...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
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更新日期：2012-08-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
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更新日期：2008-08-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2007.07.014
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.07.001
更新日期：2009-11-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.06.022
更新日期：2014-10-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.01.001
更新日期：2014-04-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章,评审
doi：10.1016/j.ympev.2014.01.026
更新日期：2014-05-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.03.008
更新日期：2005-10-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.05.011
更新日期：2017-08-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.07.015
更新日期：2010-11-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2003.11.019
更新日期：2004-07-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.09.006
更新日期：2016-01-01 00:00:00
abstract：:We examined variation in mitochondrial control region (Domain I) sequences in three distantly related species of birds found on multiple islands in Vanuatu: the Buff-banded Rail Gallirallus philippensis (n=21, 433bp), the Emerald Dove Chalcophaps indica (n=21, 513bp), and the Streaked Fantail Rhipidura spilodera (n=17...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2006.12.013
更新日期：2007-04-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/s1055-7903(02)00325-1
更新日期：2003-02-01 00:00:00
abstract：:Taxonomy and phyletic relationships of the European termites of the holarctic genus Reticulitermes are highly debated and poorly known. Sequencing analyses of the complete cytochrome oxidase subunit II and of a fragment of 16S rDNA mitochondrial genes were performed on 21 Italian and French populations. Distance, pars...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.2001.1068
更新日期：2002-03-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2003.09.004
更新日期：2004-05-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.11.005
更新日期：2019-03-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.08.016
更新日期：2014-12-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.2001.1045
更新日期：2002-02-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1999.0638
更新日期：1999-10-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2007.11.024
更新日期：2008-02-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2012.09.030
更新日期：2013-01-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.06.004
更新日期：2005-09-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.01.017
更新日期：2009-05-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2019.01.023
更新日期：2019-06-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.10.021
更新日期：2009-01-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.12.021
更新日期：2016-04-01 00:00:00
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journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.11.026
更新日期：2011-02-01 00:00:00
abstract：:Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.07.012
更新日期：2018-11-01 00:00:00
