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 Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes. RESULTS:The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder. CONCLUSIONS:Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zou H,Jakovlić I,Chen R,Zhang D,Zhang J,Li WX,Wang GTdoi
10.1186/s12864-017-4237-xsubject
Has Abstractpub_date
2017-11-02 00:00:00pages
840issue
1issn
1471-2164pii
10.1186/s12864-017-4237-xjournal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1173
更新日期:2014-12-23 00:00:00
abstract:BACKGROUND:Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive development and to elucidate the dynamic regulation of the transcriptomic response during the early-juv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5232-6
更新日期:2018-11-19 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:Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-58
更新日期:2010-01-22 00:00:00
abstract:BACKGROUND:The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2540-6
更新日期:2016-03-03 00:00:00
abstract:BACKGROUND:Streptococcus agalactiae (group B Streptococcus; GBS) is a significant bacterial pathogen of neonates and an emerging pathogen of adults. Though transcriptional regulators are abundantly encoded on the GBS genome, their role in GBS pathogenesis is poorly understood. The mtaR gene encodes a putative LysR-type...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-607
更新日期:2008-12-16 00:00:00
abstract:BACKGROUND:Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looke...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-892
更新日期:2014-10-13 00:00:00
abstract:BACKGROUND:To date several studies have sought to catalog the full suite of antibodies that humans naturally produce against single antigens or other specificities (repertoire). Here we analyze the properties of all sequenced repertoires in order to better understand the specificity of antibody responses. Specifically,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-148
更新日期:2005-10-28 00:00:00
abstract:BACKGROUND:Lysophosphatidic acid (LPA) is a lipid mediator that acts through specific G protein-coupled receptors to stimulate the proliferation, migration and survival of many cell types. LPA signaling has been implicated in development, wound healing and cancer. While LPA signaling pathways have been studied extensiv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-387
更新日期:2008-08-14 00:00:00
abstract:BACKGROUND:CRISPR-Cas9 is a revolutionary genome editing technique that allows for efficient and directed alterations of the eukaryotic genome. This relatively new technology has already been used in a large number of 'loss of function' experiments in cultured cells. Despite its simplicity and efficiency, screening for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1002
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-222
更新日期:2006-08-31 00:00:00
abstract:BACKGROUND:Accurate HLA typing at amino acid level (four-digit resolution) is critical in hematopoietic and organ transplantations, pathogenesis studies of autoimmune and infectious diseases, as well as the development of immunoncology therapies. With the rapid adoption of genome-wide sequencing in biomedical research,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-325
更新日期:2014-05-01 00:00:00
abstract:BACKGROUND:Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches for protein structure comparison apply the secondary structure elements (SSEs) representation of prot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S2-S1
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-120
更新日期:2012-03-28 00:00:00
abstract:BACKGROUND:Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, inc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-796
更新日期:2013-11-15 00:00:00
abstract:BACKGROUND:Lychas mucronatus is one scorpion species widely distributed in Southeast Asia and southern China. Anything is hardly known about its venom components, despite the fact that it can often cause human accidents. In this work, we performed a venomous gland transcriptome analysis by constructing and screening th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-452
更新日期:2010-07-28 00:00:00
abstract:BACKGROUND:Triptolide is a therapeutic diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. Triptolide has been shown to induce apoptosis by activation of pro-apoptotic proteins, inhibiting NFkB and c-KIT pathways, suppressing the Jak2 transcription, activating MAPK8/JNK signaling and modulating the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1614-1
更新日期:2015-06-30 00:00:00
abstract:BACKGROUND:Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3' end sequencing provides a valuable data source for the study o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5433-7
更新日期:2019-01-22 00:00:00
abstract:BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-132
更新日期:2014-02-14 00:00:00
abstract:BACKGROUND:Protein phosphorylation by kinases plays crucial roles in various biological processes including signal transduction and tumorigenesis, thus a better understanding of protein phosphorylation events in cells is fundamental for studying protein functions and designing drugs to treat diseases caused by the malf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06895-2
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4570-8
更新日期:2018-03-06 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:Clock genes are considered to be the molecular core of biological clock in vertebrates and they are directly involved in the regulation of daily rhythms in vertebrate tissues such as skeletal muscles. Fish myotomes are composed of anatomically segregated fast and slow muscle fibers that possess different met...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3373-z
更新日期:2016-12-08 00:00:00
abstract:BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-10
更新日期:2014-01-05 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular sys...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3907-z
更新日期:2017-07-19 00:00:00
abstract:BACKGROUND:Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koala...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-667
更新日期:2014-08-08 00:00:00
abstract:BACKGROUND:Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-515
更新日期:2008-10-31 00:00:00
abstract:BACKGROUND:Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A-G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2502-z
更新日期:2016-03-03 00:00:00
abstract:BACKGROUND:Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree tran...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-207
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06904-4
更新日期:2020-07-20 00:00:00