Abstract:
BACKGROUND:Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS:In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS:We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Schubert M,Ginolhac A,Lindgreen S,Thompson JF,Al-Rasheid KA,Willerslev E,Krogh A,Orlando Ldoi
10.1186/1471-2164-13-178subject
Has Abstractpub_date
2012-05-10 00:00:00pages
178issn
1471-2164pii
1471-2164-13-178journal_volume
13pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton's content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6268-y
更新日期:2019-11-21 00:00:00
abstract:BACKGROUND:The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-183
更新日期:2014-03-10 00:00:00
abstract:BACKGROUND:The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-544
更新日期:2012-10-10 00:00:00
abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1679-x
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5271-z
更新日期:2018-11-28 00:00:00
abstract:BACKGROUND:Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC co...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-464
更新日期:2010-08-06 00:00:00
abstract:BACKGROUND:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activati...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2169-x
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-178
更新日期:2013-03-15 00:00:00
abstract:BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6004-7
更新日期:2019-08-12 00:00:00
abstract:BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-473
更新日期:2012-09-12 00:00:00
abstract:BACKGROUND:Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-438
更新日期:2009-09-17 00:00:00
abstract:BACKGROUND:Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different families do not cooperate, but they independently fight for their survival in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-219
更新日期:2008-05-14 00:00:00
abstract:BACKGROUND:The ascomycete fungus Zymoseptoria tritici (synonyms: Mycosphaerella graminicola, Septoria tritici) is a major pathogen of wheat that causes the economically important foliar disease Septoria tritici blotch. Despite its importance as a pathogen, little is known about the reaction of this fungus to light. To ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06899-y
更新日期:2020-07-25 00:00:00
abstract:BACKGROUND:During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and pancreas. Early in organogenesis the fetal liver is populated by hematopoietic stem cells, the sourc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-33
更新日期:2012-01-19 00:00:00
abstract:BACKGROUND:Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it infects potato tubers causing internal as well as external defects, thereby reducing the market val...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6257-1
更新日期:2019-11-28 00:00:00
abstract:BACKGROUND:Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copie...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1860-2
更新日期:2015-09-03 00:00:00
abstract:BACKGROUND:Chemosensory receptors including olfactory receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) play a central role in sensing chemical signals and guiding insect behaviours, and are potential target genes in insect pest control. The cotton bollworm Helicoverpa armigera is one of the mos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-597
更新日期:2014-07-15 00:00:00
abstract:BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4349-3
更新日期:2017-12-02 00:00:00
abstract:BACKGROUND:Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07300-8
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5827-6
更新日期:2019-05-30 00:00:00
abstract:BACKGROUND:Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an inverse relationship between evolutionary constraint and the allele frequency of a mutation segregatin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-495
更新日期:2013-07-23 00:00:00
abstract:BACKGROUND:The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-335
更新日期:2014-05-04 00:00:00
abstract::ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-018-4614-0
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) has significantly impaired this proces...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1982-6
更新日期:2015-11-03 00:00:00
abstract:BACKGROUND:5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous cop...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2084-1
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallani...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4237-x
更新日期:2017-11-02 00:00:00
abstract:BACKGROUND:The androgen receptor plays a critical role throughout the progression of prostate cancer and is an important drug target for this disease. While chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) is becoming an essential tool for studying transcription and chromatin modifica...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-355
更新日期:2012-07-31 00:00:00
abstract:BACKGROUND:Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. RESULTS:Here we report a novel nanowell-based single-cell RNA...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3893-1
更新日期:2017-07-07 00:00:00
abstract:BACKGROUND:Decapods are an order of crustaceans which includes shrimps, crabs, lobsters and crayfish. They occur worldwide and are of great scientific interest as well as being of ecological and economic importance in fisheries and aquaculture. However, our knowledge of their biology mainly comes from the group which i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6433-3
更新日期:2020-01-09 00:00:00
abstract:BACKGROUND:Uranium (U) is a naturally occurring radionuclide that has been found in the aquatic environment due to anthropogenic activities. Exposure to U may pose risk to aquatic organisms due to its radiological and chemical toxicity. The present study aimed to characterize the chemical toxicity of U in Atlantic salm...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-694
更新日期:2014-08-20 00:00:00