Abstract:
BACKGROUND:The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis-regulatory element (CRE) maps that had previously been generated for A. aegypti. RESULTS:We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to create an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. CONCLUSION:Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies.
journal_name
Hereditasjournal_title
Hereditasauthors
Nowling RJ,Behura SK,Halfon MS,Emrich SJ,Duman-Scheel Mdoi
10.1186/s41065-021-00172-2subject
Has Abstractpub_date
2021-01-28 00:00:00pages
7issue
1eissn
0018-0661issn
1601-5223pii
10.1186/s41065-021-00172-2journal_volume
158pub_type
杂志文章相关文献
HEREDITAS文献大全abstract::It has been reported that oxidative stress is a factor in cerebral infarction (CI). Extracellular superoxide dismutase (EC-SOD) is important in preventing oxidative stress, and the cerebral infarct size of EC-SOD knockout mice is significantly larger than that in wild-type controls. The aim of this study was to invest...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2008.02086.x
更新日期:2008-12-01 00:00:00
abstract::The Tradescantia/micronuclei test (TRAD/MCN) is a well-validated test for monitoring environmental genotoxicants. These pollutants induce at the early meiotic stage of pollen mother cells chromosome fragments which become micronuclei at the tetrad stage. The standard test protocol requires some hours of exposure of th...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2000.t01-1-00171.x
更新日期:2000-01-01 00:00:00
abstract::Chromosomal rearrangements have played a key role in the speciation of the New World sexual Artemia species (Crustacea, Anostraca) A. franciscana and A. persimilis. The species differ by a chromosome duplication (2n+2=44 in A. persimilis vs 2n=42 in A. franciscana), and a greater amount of heterochromatin (HCH) in A. ...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2009.02109.x
更新日期:2009-05-01 00:00:00
abstract::In this study, cytogenetic analysis of an infertile mare revealed a 64, XY karyotype. The XY sex-reversed animal had a female phenotype with gonadal dysgenesis. Using Southern blot analysis, we tested for the presence of two Y-specific genes SRY and ZFY by using DNA isolated from peripheral blood leukocytes. The resul...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1995.00109.x
更新日期:1995-01-01 00:00:00
abstract::Chromosomes were studied in cultured material from two different areas of a human mucoepidermoid carcinoma. The detailed banding analyses showed no less than 41 different karyotypes. Comparisons between these revealed (1) that the tumour probably had originated with a normal, diploid stemline; (2) that the progression...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1989.tb00420.x
更新日期:1989-01-01 00:00:00
abstract::Partial amphiploids between wheat (Triticum aestivum L.) and Thinopyrum species play an important role in the transfer and use of traits from alien species. A wheat-Thinopyrum intermedium partial amphiploid, TAI8335, and its alien parent were characterized by a combination of genomic in situ hybridization (GISH) and c...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2010.02156.x
更新日期:2010-12-01 00:00:00
abstract::Microsatellites have become the most important class of markers for mapping procedures. Primarily based on restriction fragment length polymorphism (RFLP) markers, several molecular genetic maps of maize have been developed, mainly using temperate inbred maize lines. To characterize the level of polymorphism of micros...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2003.01666.x
更新日期:2003-01-01 00:00:00
abstract:Background:Genealogy and molecular genetic studies of a Swedish river valley population resulted in a large pedigree, showing that the hereditary hemochromatosis (HH) HFE/p.C282Y mutation is inherited with other recessive disorders such as Wilson´s disease (WND), a rare recessive disorder of copper overload. The popula...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-017-0052-2
更新日期:2017-12-19 00:00:00
abstract:BACKGROUND:While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass. RESULTS:In this study, a genome-wide association study...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-017-0027-3
更新日期:2017-02-23 00:00:00
abstract::Physical locations of 45S and 5S rDNA were detected in maize by fluorescence in situ hybridization (FISH). The FISH results on metaphase chromosome spreads showed the 45S rDNA was located just at the nucleolus organizer region (NOR) on 6S (the short arm) of chromosome 6) as expected, and 5S rDNA at the distal region o...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2001.00141.x
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:Seven in absentia homolog 1 (SIAH1) is an E3 ubiquitin ligase containing a RING-finger domain and a key regulator of normal development. Skin and hair follicle development is a complex and special process of morphogenesis involving multiple signaling pathways. SIAH1 is enriched in the Wnt signaling pathway a...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-020-00126-0
更新日期:2020-04-06 00:00:00
abstract::A PCR-amplified DNA, cMWG699, is linked to the vrs1 (formerly v) locus controlling 2- and 6-rowed spikelets. Restriction analysis of the amplified DNA of 65 varieties from Europe, America, and East Asia revealed 3 alleles, named types K, A and D. Two-rowed varieties were mostly of type K allele, and 6-rowed varieties ...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1999.00077.x
更新日期:1999-01-01 00:00:00
abstract::Five new cases of reciprocal translocation in the domestic pig are described. Three of them, rep(3;5)(p1.3;q2.3), rep(6;13)(p1.5;q4.1) and rep(13;17)(q4.1;q1.1) were found in boars with decreased litter size. The remaining two were identified in animals karyotyped before reproduction: a young boar, rep(4;6)(q2.1;q2.8)...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1998.00221.x
更新日期:1998-01-01 00:00:00
abstract::This paper provides new data on chromosomes of Brazilian vampire bats Desmodus rotundus and Diphylla ecaudata. These species were analyzed by GTG, CBG- and CB-DAPI banding, AgNO3/CMA3 sequential staining, base-specific fluorochrome dyes and in situ hybridization with 18S rDNA probe. C-banding (CBG) revealed constituti...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2001.00189.x
更新日期:2001-01-01 00:00:00
abstract::In several branches derived from an inbred line of Drosophila melanogaster, transitions from R- to I-type in the I-R system have been observed. After a recent split into two branches of an R-type (+)-K subline, one branch showed, on retesting, an alteration to I-type. Genome from the R-type (+)-K branch was introduced...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1990.tb00066.x
更新日期:1990-01-01 00:00:00
abstract::Within and among populations genetic variance of twelve Hemarthria compressa populations and one Hemarthria japonica population from China were analyzed using inter simple sequence repeat (ISSR). Twelve primers amplified a total of 165 genomic DNA fragments across a total of 148 individuals of which 156 were polymorph...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.0018-0661.2008.02031.x
更新日期:2008-04-01 00:00:00
abstract::Alloploids, most of them hexaploid, from crosses between tetraploid wheat, Triticum carthlicum, and the perennial tetraploid Thinopyrum junceiforme were analysed for chromosome composition, stability and fertility using genomic in situ hybridization and meiotic analysis. The alloploids differed in their total number o...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1034/j.1601-5223.2002.1360109.x
更新日期:2002-01-01 00:00:00
abstract::Meiotic studies are carried out in 7 species of Eryngium L. (Saniculoideae, Apiaceae), belonging to both sections Foetida and Panniculata. The chromosome number of E. dorae Norm. (n=8) (Foetida) is reported for the first time, while the gametic chromosome number of E. nudicaule Lam. (n=7) (Foetida) and E. eburneum Dec...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2004.01795.x
更新日期:2004-01-01 00:00:00
abstract::The dogroses, Rosa section Caninae, are all polyploid and characterised by their unbalanced meiosis; the pollen parent contributes one genome, whereas the seed parent contributes 3-5 genomes depending upon ploidy level of the species. As a result, genetically determined traits are expected to be matroclinally inherite...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2001.00001.x
更新日期:2001-01-01 00:00:00
abstract:Background:Recent large-scale genome-wide association studies (GWAS) have showed that the neuronal calcium signaling has pivotal roles in schizophrenia (SCZ) in populations of European of ancestry. However, it is not known if calcium signaling pathway genes are also associated with SCZ in Han Chinese population. Metho...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-017-0054-0
更新日期:2018-01-02 00:00:00
abstract::In general, cyclins control the cell cycle. Not so the atypical cyclins, which are required for diverse cellular functions such as for genome stability or for the regulation of transcription and translation. The atypical Cyclin G (CycG) gene of Drosophila has been involved in the epigenetic regulation of abdominal seg...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2012.02273.x
更新日期:2012-10-01 00:00:00
abstract::The highly invasive Chinese mitten crabs (Eriocheir sinensis) was studied to reveal the genetic relationship between three none self-sustainable population within the Polish Oder and Vistula River and Lake Vänern in Sweden. Crabs from self-sustainable populations were collected from the Elbe River (Germany), San Franc...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2012.02246.x
更新日期:2012-04-01 00:00:00
abstract::Amplified fragment length polymorphism (AFLP) DNA markers were used to characterize the genetic diversity and relationships in wild species of the genus Aegilops. Fifty populations, which included the species Aegilops biuncialis (UUMM), Ae. neglecta (UUMMNN), Ae. ovata (UUMM), Ae. ventricosa (DDNN) and Ae. triuncialis...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2001.00233.x
更新日期:2001-01-01 00:00:00
abstract:Background:Cervical cancer is a malignancy that's common in female with high incidence and mortality worldwide. MicroRNAs (miRNAs) act a pivotal part in human cancer development. Our aim was to investigate the effect of miR-126 on cervical cancer and its underlying molecular mechanism. Results:Firstly, RT-qPCR assay r...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-019-0087-7
更新日期:2019-04-09 00:00:00
abstract::The current work describes, for the first time, the occurrence of B chromosomes in the genus Pimelodus. Cytogenetic analysis in P. ortmanni and Pimelodus sp., from the river Iguaçu basin, revealed a diploid number of 56 chromosomes. Whereas distribution pattern of C-banding in Pimelodus sp. showed predominance of hete...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.2004.01812.x
更新日期:2004-01-01 00:00:00
abstract::Temperature sensitive experiments on the interaction of Abruptex mutations of the Notch locus and Enhancer of split indicate that the effect of temperature on the development of macrochaeta and wing venation is different. This suggest that Notch affects the development of macrochaeta and wing venation in different and...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1998.t01-1-00251.x
更新日期:1998-01-01 00:00:00
abstract::Synaptonemal complex analysis, by electron microscopy of spread spermatocytes after phosphotungstic acid staining, made possible description of the chromosomal synaptic patterns and the synaptonemal complex karyotype of the pig (Sus scrofa domestica). The autosomal synaptic pattern in conjunction with the sex chromoso...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1993.t01-3-00087.x
更新日期:1993-01-01 00:00:00
abstract::Behaviour of acrocentric chromosome synaptonemal complexes (SCs) and constitutive heterochromatin (C-band) during meiotic prophase I of the male domestic pig was studied using surface spreading and silver staining techniques. At late zygotene C-band regions of complete or incomplete SCs of the acrocentric chromosomes ...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1990.tb00065.x
更新日期:1990-01-01 00:00:00
abstract:Background:Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers and represent the foundation for their formation, processing and utilization of yield; and are a...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1186/s41065-019-0086-8
更新日期:2019-02-06 00:00:00
abstract::On the assumption that the survival of a parthenogenetic strain in nature relies on the strain's ability to compete with the bisexual population, we attempted to discern any diminution of competition between bisexual strains of Drosophila and parthenogenetic strains derived from them on the basis of light intensity pr...
journal_title:Hereditas
pub_type: 杂志文章
doi:10.1111/j.1601-5223.1992.tb00018.x
更新日期:1992-01-01 00:00:00