scholarly journals A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence

2003 ◽  
Vol 13 (8) ◽  
pp. 1966-1972 ◽  
Author(s):  
Denis M. Larkin ◽  
Annelie Everts-van der Wind ◽  
Mark Rebeiz ◽  
Peter A. Schweitzer ◽  
Sharon Bachman ◽  
...  
Keyword(s):  
Mouse Genome ◽  
Read Length ◽  
Evolutionary Analysis ◽  
Cattle Genome ◽  
Average Read Length ◽  
Bac Clone ◽  
Comparative Map ◽  
End Sequences ◽  
Rh Panel ◽  
Human And Mouse

As a step toward the goal of adding the cattle genome to those available for multispecies comparative genome analysis, 40,224 cattle BAC clones were end-sequenced, yielding 60,547 sequences (BAC end sequences, BESs) after trimming with an average read length of 515 bp. Cattle BACs were anchored to the human and mouse genome sequences by BLASTN search, revealing 29.4% and 10.1% significant hits (E < e-5), respectively. More than 60% of all cattle BES hits in both the human and mouse genomes are located within known genes. In order to confirm in silico predictions of orthology and their relative position on cattle chromosomes, 84 cattle BESs with similarity to sequences on HSA11 were mapped using a cattle–hamster radiation hybrid (RH) panel. Resulting RH maps of BTA15 and BTA29 cover ∼85% of HSA11 sequence, revealing a complex patchwork shuffling of segments not explained by a simple translocation followed by internal rearrangements. Overlay of the mouse conserved syntenies onto HSA11 revealed that segmental boundaries appear to be conserved in all three species. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.

Substitution pattern of the CArG element in human and mouse genomes

Genome ◽  
2011 ◽  
Vol 54 (2) ◽  
pp. 144-150 ◽  
Author(s):  
Xia Shen ◽  
Haimei Mao ◽  
Shan Miao
Keyword(s):  
Mouse Genome ◽  
Serum Response Factor ◽  
Statistical Tests ◽  
Evolutionary Analysis ◽  
Substitution Pattern ◽  
Functional Assays ◽  
The Core ◽  
Tata Motif ◽  
Serum Response ◽  
Human And Mouse

cis-Elements CArG bound by serum response factor (SRF) are presently being intensively studied, but little is known about the substitution pattern of functional CArG elements. Here, we have performed the first evolutionary analysis of CArGome in the human and mouse genome through bioinformatic methods and statistical tests. We calculated the substitution rate at each site of the functional CArG elements. The results showed that the core sites of the functional CArG elements evolved faster than did the background DNA, indicating that these sites were likely to evolve under positive selection. Moreover, a strong TATA “motif” was evident in the core region within the functional CArG elements in both human and mouse promoters. This motif could probably be a major contribution to the formation of the spatial structure, which was important for CArG-SRF recognition. Thus, the study further revealed the sequence character and substitution pattern of CArG elements and provided useful information for the study of the SRF-binding efficiencies of CArG promoters in functional assays.

scholarly journals A human–horse comparative map based on equine BAC end sequences

Genomics ◽  
2006 ◽  
Vol 87 (6) ◽  
pp. 772-776 ◽  
Author(s):  
Tosso Leeb ◽  
Claus Vogl ◽  
Baoli Zhu ◽  
Pieter J. de Jong ◽  
Matthew M. Binns ◽  
...  
Keyword(s):  
Comparative Map ◽  
End Sequences

scholarly journals A14 Comprehensive characterisation and evolutionary analysis of endogenous retroviruses in the mouse genome

2017 ◽  
Vol 3 (suppl_1) ◽  
Author(s):  
Tristan P.W. Dennis ◽  
Henan Zhu ◽  
Sam J. Wilson ◽  
Robert J. Gifford
Keyword(s):  
Mouse Genome ◽  
Endogenous Retroviruses ◽  
Evolutionary Analysis

scholarly journals Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

2011 ◽  
Vol 77 (7) ◽  
pp. 2264-2274 ◽  
Author(s):  
Ji Young Jung ◽  
Se Hee Lee ◽  
Jeong Myeong Kim ◽  
Moon Su Park ◽  
Jin-Woo Bae ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Leuconostoc Mesenteroides ◽  
16S Rrna Genes ◽  
Read Length ◽  
Rrna Genes ◽  
Genetic Profile ◽  
Average Read Length ◽  
Metabolic Potential ◽  
Fermentation Products

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

scholarly journals Impact of Chimera-less Long Reads on Metagenomics of Human Gut Viromes Treated With Multiple Displacement Amplification

2020 ◽  
Author(s):  
Yuya Kiguchi ◽  
Suguru Nishijima ◽  
Naveen Kumar ◽  
Masahira Hattori ◽  
Wataru Suda
Keyword(s):  
De Novo ◽  
Multiple Displacement Amplification ◽  
Read Length ◽  
Human Gut ◽  
Average Read Length ◽  
Sequencing Technologies ◽  
Genomic Complexity ◽  
Long Reads ◽  
Long Read ◽  
The Impact

Abstract Background: The ecological and biological features of the indigenous phage community (virome) in the human gut microbiome are poorly understood, possibly due to many fragmented contigs and fewer complete genomes based on conventional short-read metagenomics. Long-read sequencing technologies have attracted attention as an alternative approach to reconstruct long and accurate contigs from microbial communities. However, the impact of long-read metagenomics on human gut virome analysis has not been well evaluated. Results: Here we present chimera-less PacBio long-read metagenomics of multiple displacement amplification (MDA)-treated human gut virome DNA. The method included the development of a novel bioinformatics tool, SACRA (Split Amplified Chimeric Read Algorithm), which efficiently detects and splits numerous chimeric reads in PacBio reads from the MDA-treated virome samples. SACRA treatment of PacBio reads from five samples markedly reduced the average chimera ratio from 72 to 1.5%, generating chimera-less PacBio reads with an average read-length of 1.8 kb. De novo assembly of the chimera-less long reads generated contigs with an average N50 length of 11.1 kb, whereas those of MiSeq short reads from the same samples were 0.7 kb, dramatically improving contig extension. Alignment of both contig sets generated 378 high-quality merged contigs (MCs) composed of the minimum scaffolds of 434 MiSeq and 637 PacBio contigs, respectively, and also identified numerous MiSeq short fragmented contigs ≤500 bp additionally aligned to MCs, which possibly originated from a small fraction of MiSeq chimeric reads. The alignment also revealed that fragmentations of the scaffolded MiSeq contigs were caused primarily by genomic complexity of the community, including local repeats, hypervariable regions, and highly conserved sequences in and between the phage genomes. We identified 142 complete and near-complete phage genomes including 108 novel genomes, varying from 5 to 185 kb in length, the majority of which were predicted to be Microviridae phages including several variants with homologous but distinct genomes, which were fragmented in MiSeq contigs. Conclusions: Long-read metagenomics coupled with SACRA provides an improved method to reconstruct accurate and extended phage genomes from MDA-treated virome samples of the human gut, and potentially from other environmental virome samples.

scholarly journals A new unsupervised binning method for metagenomic dataset with automated estimation of number of species

2015 ◽  
Author(s):  
Yun Liu ◽  
Tao Hou ◽  
Liu Fu
Keyword(s):  
Partition Coefficient ◽  
Experimental Results ◽  
Read Length ◽  
Species Number ◽  
Initial Number ◽  
Metagenomic Dataset ◽  
Average Read Length ◽  
Metagenome Analysis ◽  
Clustering Validity ◽  
The Relationship

One necessary step of metagenome analysis is to assign sequences to classes according to their taxonomic origins. Unsupervised binning method is one of the two binning categories. However existing unsupervised binning methods yield to estimate the species number automatically and accurately. In this paper, a new unsupervised binning method based on an improved fuzzy c-means method (iFCM) is presented for metagenomic dataset. First, a range of the number of bins is obtained by the relationship among sequencing depth, number of reads and average read length. Secondly, iFCM algorithm is implemented several times with the initial number of bins in this range. Finally, the number of bins is determined by a clustering validity, modified partition coefficient. Experimental results show that this method is an effective unsupervised binning method for metagenomic dataset and could estimate the species number more accurately than MetaCluster3.0 and AbundanceBin.

scholarly journals A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Martin Pippel ◽  
David Jebb ◽  
Franziska Patzold ◽  
Sylke Winkler ◽  
Heiko Vogel ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Annotation ◽  
Incomplete Lineage Sorting ◽  
Read Length ◽  
Ecological Niches ◽  
Average Read Length ◽  
General Applicability ◽  
Pacific Biosciences ◽  
A Genome ◽  
Wide Range

Abstract Background Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. Results Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. Conclusions Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.

Combining semiconductor-based sequencing with amplicon-based cancer gene panels: A rapid next-gen approach to clinical cancer genotyping.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10591-10591
Author(s):  
Christopher L. Corless ◽  
Tanaya Neff ◽  
Michael C. Heinrich ◽  
Carol Beadling
Keyword(s):  
Point Mutations ◽  
Read Length ◽  
Cancer Genes ◽  
Automated Identification ◽  
Average Read Length ◽  
Clinical Cancer ◽  
Multiplexed Pcr ◽  
Next Gen Sequencing ◽  
Gene Panels ◽  
Personalized Cancer

10591 Background: Bringing next-gen sequencing into clinical (CLIA-licensed) laboratories is an important step in the advancement of personalized cancer care. We have validated a new sequencing approach on the Ion Torrent (IT) PGM using the AmpliSeq Cancer Panel, which covers hotspot regions across 46 commonly mutated cancer genes. Methods: The AmpliSeq panel is comprised of 190 primer pairs that are co-amplified in a single tube to generate amplicons for sequencing. In our testing only 10ng of input DNA was used. Initial PCR was for 20 cycles, after which the amplicons were ligated with sequencing/barcode adapters, amplified for an additional 7 cycles, and then subjected to emulsion PCR. The resulting nanospheres were sequenced on an IT 316 chip. Results: We sequenced 44 samples of FFPE-derived tumor DNA that were previously genotyped on a mass spectroscopy (MS)-based panel. Samples were barcoded and sequenced in batches of 4, yielding an average of 2034 reads per amplicon (range: 95-5162) and an average read length of 76bp. Overall, 95.4% of reads were on target, and 79% of reads were AQ20 or better; 95% of the 190 amplicons had over 500 reads. All 42 known point mutations were accurately identified by the variant caller software. Seventeen in/dels from 4 to 63 bp in length were at least partially visible upon manual inspection of the read alignments, but some were not accurately called by the software. In addition, 22 new mutations were identified in gene regions not covered on our MS-based panel. We demonstrated sensitivity to the level of 5% mutant allele, and the correlation between allelic ratios measured by MS and IT sequencing was excellent (r2=0.81). Two DNA samples from laser-captured tumor worked well with the AmpliSeq Panel. Conclusions: Combining solid-state sequencing with a highly multiplexed PCR method for library construction is a rapid (48 hr) approach for next-gen sequencing of clinical cancer samples. The process is highly scalable and larger, cancer-specific amplicon panels are in development. Automated identification of in/dels remains a challenge in next-gen sequencing output.

Isopentenyl-Diphosphate Isomerases in Human and Mouse: Evolutionary Analysis of a Mammalian Gene Duplication

2003 ◽  
Vol 57 (3) ◽  
pp. 282-291 ◽  
Author(s):  
Rainer Breitling ◽  
Daniela Laubner ◽  
Daun Clizbe ◽  
Jerzy Adamski ◽  
Skaidrite K. Krisans
Keyword(s):  
Gene Duplication ◽  
Evolutionary Analysis ◽  
Isopentenyl Diphosphate ◽  
Mammalian Gene ◽  
Human And Mouse
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