Abstract:
BACKGROUND:Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week. RESULTS:Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression. CONCLUSION:This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Armstrong AF,Grosberg RKdoi
10.1186/s12864-018-4768-9subject
Has Abstractpub_date
2018-05-18 00:00:00pages
368issue
1issn
1471-2164pii
10.1186/s12864-018-4768-9journal_volume
19pub_type
杂志文章相关文献
BMC GENOMICS文献大全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:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3215-z
更新日期:2016-11-04 00:00:00
abstract:BACKGROUND:The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1867-8
更新日期:2015-09-02 00:00:00
abstract:BACKGROUND:Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chick...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-441
更新日期:2012-08-31 00:00:00
abstract:BACKGROUND:Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. RESULTS:We have used array comparative genomic hybridization (aCGH)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-62
更新日期:2010-01-25 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:The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that the canonical single chromosome with 37 genes found in almost all other bilaterians has been lost in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-394
更新日期:2011-08-04 00:00:00
abstract:BACKGROUND:Epstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV. RESULTS:Novel EBV RNAs and RN...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-543
更新日期:2013-08-09 00:00:00
abstract:BACKGROUND:Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and he...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2928-3
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07267-6
更新日期:2020-11-27 00:00:00
abstract:BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4079-6
更新日期:2017-08-31 00:00:00
abstract:BACKGROUND:Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound ada...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6152-9
更新日期:2019-11-20 00:00:00
abstract:BACKGROUND:Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-546
更新日期:2013-08-12 00:00:00
abstract:BACKGROUND:Recent studies have shown that human populations have experienced a complex demographic history, including a recent epoch of rapid population growth that led to an excess in the proportion of rare genetic variants in humans today. This excess can impact the burden of private mutations for each individual, de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S4-S3
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S8-S8
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Wheat is the most important staple crop in Afghanistan and accounts for the main part of cereal production. However, wheat production has been unstable during the last decades and the country depends on seed imports. Wheat research in Afghanistan has emphasized releases of new, high-yielding and disease resi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6015-4
更新日期:2019-08-19 00:00:00
abstract:BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S1-S20
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6552-x
更新日期:2020-02-11 00:00:00
abstract:BACKGROUND:The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in Schwann cells and is therefore a context-dependent, pro-myelination transcription factor. As such, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3167-3
更新日期:2016-11-07 00:00:00
abstract:BACKGROUND:Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5214-8
更新日期:2018-11-29 00:00:00
abstract:BACKGROUND:The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6600-6
更新日期:2020-03-23 00:00:00
abstract:BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-611
更新日期:2014-07-19 00:00:00
abstract:BACKGROUND:Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and functio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06942-y
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2447-2
更新日期:2016-02-18 00:00:00
abstract:BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S5-S5
更新日期:2011-12-23 00:00:00
abstract:BACKGROUND:Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3471-y
更新日期:2017-01-13 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:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S2-S5
更新日期:2012-04-12 00:00:00
abstract:BACKGROUND:Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3257-2
更新日期:2017-01-25 00:00:00
abstract:BACKGROUND:Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a criti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5329-y
更新日期:2018-12-07 00:00:00