Abstract:
BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insight into the ecology, evolution, nutritional and medical properties of this highly adaptable organism, are missing. In this work, using next-generation sequencing (NGS) techniques we assessed a significant portion of the transcriptome of this non-model organism. RESULTS:Out of the 9445 de novo assembled contigs, 2886 (30.6%) returned significant hits and for 2261 (24%) of them Gene Ontology (GO) terms associated to the hits were retrieved. A high percentage of the contigs (69.4%) produced no BLASTx hits. The GO terms were grouped to reflect biological processes, molecular functions and cellular components. Certain GO terms were dominant in all groups. After scanning the assembled transcriptome for microsatellites (simple sequence repeats, SSRs), a total of 563 SSRs were recovered. Among the identified SSRs, trinucleotide repeats were the predominant followed by tetranucleotide and dinucleotide repeats. CONCLUSION:The annotation success of the transcriptome of C. aspersum was relatively low. This is probably due to the very limited number of annotated reference genomes existing for mollusc species, especially terrestrial ones. Several biological processes being active in the aestivating species were revealed through the association of the transcripts to enzymes relating to the pathways. The genomic tools provided herein will eventually aid in the study of the global genomic diversity of the species and the investigation of aspects of the ecology, evolution, behavior, nutritional and medical properties of this highly adaptable organism.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Parmakelis A,Kotsakiozi P,Kontos CK,Adamopoulos PG,Scorilas Adoi
10.1186/s12864-017-3885-1subject
Has Abstractpub_date
2017-06-28 00:00:00pages
491issue
1issn
1471-2164pii
10.1186/s12864-017-3885-1journal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-347
更新日期:2013-05-24 00:00:00
abstract:BACKGROUND:Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. RESULTS:Here, we systematically assessed the utility of paired-end and mat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-257
更新日期:2013-04-16 00:00:00
abstract:BACKGROUND:Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA meth...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-698
更新日期:2014-08-20 00:00:00
abstract:BACKGROUND:Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgut proteins and their potential role in refractoriness for malaria control in Anopheles mosquitoes. T...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4729-3
更新日期:2018-05-08 00:00:00
abstract:BACKGROUND:Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangem...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S15
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2083-2
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-241
更新日期:2009-05-22 00:00:00
abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-686
更新日期:2013-10-06 00:00:00
abstract:BACKGROUND:Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5418-y
更新日期:2019-01-16 00:00:00
abstract:BACKGROUND:While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses on four Listeria monocytogenes, including human and food isolates from both a 1988 case of sporadic...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-539
更新日期:2008-11-13 00:00:00
abstract:BACKGROUND:Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-381
更新日期:2012-08-08 00:00:00
abstract:BACKGROUND:Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD rep...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5135-6
更新日期:2018-11-08 00:00:00
abstract:BACKGROUND:Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data gener...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2614-5
更新日期:2016-04-14 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:It is believed that the main factors of low prenatal growth in mammals are genetic and environmental. We used isogenic mice maintained in standard conditions to analyze how natural non-genetic microsomia (low birth weight) is produced in inbred mice and its long term effect on health. To better understand th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-327
更新日期:2014-05-01 00:00:00
abstract:BACKGROUND:Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4967-4
更新日期:2018-08-06 00:00:00
abstract:BACKGROUND:Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e.,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S13-S5
更新日期:2015-01-01 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:Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the embryo-to-hatchling transition. Furthermore, we know very little about the metabolic and regulatory fac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5080-4
更新日期:2018-09-21 00:00:00
abstract:BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5618-0
更新日期:2019-03-27 00:00:00
abstract:BACKGROUND:Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5203-y
更新日期:2018-11-07 00:00:00
abstract:BACKGROUND:Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5346-x
更新日期:2018-12-20 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS:We prop...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-409
更新日期:2014-05-28 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:We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the partici...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-109
更新日期:2005-08-17 00:00:00
abstract:BACKGROUND:Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. RESULTS:In this study, we constructed a high-density genetic map of the P...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07254-x
更新日期:2020-12-02 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:Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6339-0
更新日期:2019-12-11 00:00:00
abstract:BACKGROUND:Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulating cell cycle progression and apoptosis both positively and negatively. However, it still remains to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-275
更新日期:2012-06-22 00:00:00