Abstract:
BACKGROUND:Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to the extreme sequence divergence of many genes and the difficulty of obtaining pure samples: exogenous DNA from ingested food or ecto/endo symbionts often vastly exceed the amount of "native" DNA, and foraminiferans cannot be cultured axenically. Few foraminiferal genes have been sequenced from genomic material, although partial sequences of coding regions have been determined by EST studies and mass spectroscopy. The lack of genomic data has impeded evolutionary and cell-biology studies and has also hindered our ability to test ecological hypotheses using genetic tools. RESULTS:454 sequence analysis was performed on a library derived from whole genome amplification of microdissected nuclei of the Antarctic foraminiferan Astrammina rara. Xenogenomic sequence, which was shown not to be of eukaryotic origin, represented only 12% of the sample. The first foraminiferal examples of important classes of genes, such as tRNA genes, are reported, and we present evidence that sequences of mitochondrial origin have been translocated to the nucleus. The recovery of a 3' UTR and downstream sequence from an actin gene suggests that foraminiferal mRNA processing may have some unusual features. Finally, the presence of a co-purified bacterial genome in the library also permitted the first calculation of the size of a foraminiferal genome by molecular methods, and statistical analysis of sequence from different genomic sources indicates that low-complexity tracts of the genome may be endoreplicated in some stages of the foraminiferal life cycle. CONCLUSIONS:These data provide the first window into genomic organization and genetic control in these organisms, and also complement and expands upon information about foraminiferal genes based on EST projects. The genomic data obtained are informative for environmental and cell-biological studies, and will also be useful for efforts to understand relationships between foraminiferans and other protists.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Habura A,Hou Y,Reilly AA,Bowser SSdoi
10.1186/1471-2164-12-169subject
Has Abstractpub_date
2011-03-31 00:00:00pages
169issn
1471-2164pii
1471-2164-12-169journal_volume
12pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S11
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3990-1
更新日期:2017-08-16 00:00:00
abstract:BACKGROUND:Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4708-8
更新日期:2018-05-21 00:00:00
abstract:BACKGROUND:Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are located in a 2 Mb range of the human chromosome 8p23.1. This DEF locus, however, represents one of the regions in the euchromatic part ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-92
更新日期:2004-12-10 00:00:00
abstract:BACKGROUND:The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AM...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-385
更新日期:2007-10-23 00:00:00
abstract:BACKGROUND:The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential roles in contributing to their overall health and production performance. In the present study, RNA se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6320-y
更新日期:2019-12-12 00:00:00
abstract:BACKGROUND:There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-411
更新日期:2012-08-20 00:00:00
abstract:BACKGROUND:The completion of the Plasmodium falciparum genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-255
更新日期:2007-07-27 00:00:00
abstract:BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6391-9
更新日期:2019-12-26 00:00:00
abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/s12864-017-3862-8
更新日期:2017-06-27 00:00:00
abstract:BACKGROUND:Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets of protein-coding genes were selected from pre-existing microarray data: (1) those whose expressio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-110
更新日期:2005-08-17 00:00:00
abstract:BACKGROUND:Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work toget...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4160-1
更新日期:2017-11-07 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:White spot syndrome (WSS) is a viral disease that affects most of the commercially important shrimps and causes serious economic losses to the shrimp farming industry worldwide. However, little information is available in terms of the molecular mechanisms of the host-virus interaction. In this study, we used...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-120
更新日期:2007-05-16 00:00:00
abstract:BACKGROUND:As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-730
更新日期:2013-10-25 00:00:00
abstract:BACKGROUND:By assaying hundreds of thousands of single nucleotide polymorphisms, genome wide association studies (GWAS) allow for a powerful, unbiased review of the entire genome to localize common genetic variants that influence health and disease. Although it is widely recognized that some correction for multiple tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-516
更新日期:2008-10-31 00:00:00
abstract:BACKGROUND:Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-130
更新日期:2006-05-31 00:00:00
abstract:BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-16
更新日期:2014-01-10 00:00:00
abstract:BACKGROUND:Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5657-6
更新日期:2019-04-05 00:00:00
abstract:BACKGROUND:About 10% of cases of male infertility are due to the presence of microdeletions within the long arm of the Y chromosome (Yq). Despite the large literature covering this critical issue, very little is known about the pathogenic mechanism leading to spermatogenesis disruption in patients carrying these microd...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-401
更新日期:2010-06-24 00:00:00
abstract:BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2960-3
更新日期:2016-08-11 00:00:00
abstract:BACKGROUND:Chromosome 17q21.31 contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry. Two divergent MAPT haplotypes, H1 and H2 are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. The MAPT H1 haploty...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-458
更新日期:2012-09-06 00:00:00
abstract:BACKGROUND:Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1347-1
更新日期:2015-02-28 00:00:00
abstract:BACKGROUND:Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and ph...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-469
更新日期:2012-09-11 00:00:00
abstract:BACKGROUND:Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vacci...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-143
更新日期:2012-04-24 00:00:00
abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-10-S2-I1
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-289
更新日期:2011-06-03 00:00:00
abstract:BACKGROUND:The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing')...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-21
更新日期:2010-01-11 00:00:00
abstract:BACKGROUND:Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4304-3
更新日期:2017-11-21 00:00:00
abstract:BACKGROUND:Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to Campylobacter could potentially redu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2612-7
更新日期:2016-04-18 00:00:00