Abstract:
:Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Turakhia Y,Chen HI,Marcovitz A,Bejerano Gdoi
10.1093/nar/gkaa550subject
Has Abstractpub_date
2020-09-18 00:00:00pages
e91issue
16eissn
0305-1048issn
1362-4962pii
5866417journal_volume
48pub_type
杂志文章abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.5.1081
更新日期:1980-03-11 00:00:00
abstract::Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criter...
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abstract::The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.c...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章,评审
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更新日期:1980-01-11 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1996-04-01 00:00:00
abstract::We have investigated the distribution of mitochondrial DNA polymorphisms in a rare maternally transmitted genetic trait that causes hypersensitivity to aminoglycoside antibiotics, in the hope that a characterization of its molecular basis might provide a molecular and cellular understanding of aminoglycoside-induced d...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1993-09-11 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky056
更新日期:2018-03-16 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.5.835
更新日期:1995-03-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3007
更新日期:1977-09-01 00:00:00
abstract::When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq353
更新日期:2010-10-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa023
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm246
更新日期:2007-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.5.1449
更新日期:1977-01-01 00:00:00
abstract::Staphylococcus aureus plasmid pT181 is thought to replicate via an asymmetric rolling-circle mechanism. By studying pulse labeled replicative intermediates, here we report that pT181 replication involves: (1) a post-replicative hypersupercoiled monomer and (2) a partially replicated intermediate which lacks superhelic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.2897
更新日期:1988-04-11 00:00:00
abstract::The large terminase subunit is a central component of the genome packaging motor from tailed bacteriophages and herpes viruses. This two-domain enzyme has an N-terminal ATPase activity that fuels DNA translocation during packaging and a C-terminal nuclease activity required for initiation and termination of the packag...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2013-01-07 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks683
更新日期:2012-10-01 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2013-04-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm762
更新日期:2008-01-01 00:00:00
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journal_title:Nucleic acids research
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doi:10.1093/nar/29.3.767
更新日期:2001-02-01 00:00:00
abstract::The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and r...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2016-07-27 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2004-04-23 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2014-10-01 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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