scholarly journals Genome survey and SSR analysis of Apocynum venetum

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Guo-qi Li ◽  
Li-xiao Song ◽  
Chang-qing Jin ◽  
Miao Li ◽  
Shi-pei Gong ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Size ◽  
Genome Sequencing ◽  
Repeated Sequences ◽  
Economic Plant ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Total Length ◽  
Genome Survey ◽  
Apocynum Venetum

AbstractApocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.

scholarly journals Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

2018 ◽  
Author(s):  
Maxime Garcia ◽  
Szilveszter Juhos ◽  
Malin Larsson ◽  
Pall I. Olason ◽  
Marcel Martin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Open Source ◽  
Genome Sequencing ◽  
Development Project ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Insertion And Deletion ◽  
Sample Heterogeneity

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

scholarly journals Whole-genome sequencing analysis of Y chromosome microdeletion: a case report

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052097649
Author(s):  
Zhixiang Gao ◽  
Feng Yuan ◽  
Qiaoqiao Li ◽  
Renlan Xia ◽  
Kai Fu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Y Chromosome ◽  
Genome Sequencing ◽  
Sperm Quality ◽  
Sperm Count ◽  
Therapeutic Targets ◽  
Camp Signaling ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Y Chromosome Microdeletion

The mechanisms by which Y chromosome microdeletions cause infertility have been well described; however, the therapeutic targets remain a challenge. Here, we used whole-genome sequencing to explore the mechanism of Y chromosome deletion and potential therapeutic targets in a patient with infertility. There were no abnormalities in the patient’s medical history. Routine semen analysis showed immotile sperm and only two motile spermatozoa were occasionally see after centrifugation, indicating that the direct cause of infertility was an abnormal sperm count and motility. A Y chromosome microdeletion test revealed partial deletion of the AZFc region, including AZFc1, AZFc2, AZFc3, and AZFc4. Whole-genome sequencing showed that the patient had seven harmful mutations, with only one significant epigenetic mutation, SH3KBP1. Gene Ontology analysis of these meaningful mutations indicated involvement of cAMP signaling pathways. The patient’s wife became pregnant following in vitro fertilization, and no significant abnormalities were found during prenatal examination. This case suggests that Y chromosome microdeletion and gene mutation may affect the cAMP signaling pathway, leading to reduced sperm quality and male infertility.

484 Whole Genome Sequencing Analysis of Gastroparesis

2019 ◽  
Vol 114 (1) ◽  
pp. S280-S281
Author(s):  
Sandra P. Smieszek ◽  
Jesse L. Carlin ◽  
Gunther Birznieks ◽  
Mihael H. Polymeropoulos
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Sequencing Analysis

scholarly journals Whole genome sequencing analysis of high confidence variants of B-cell lymphoma in Canis familiaris

PLoS ONE ◽  
2020 ◽  
Vol 15 (8) ◽  
pp. e0238183
Author(s):  
Alana Sparks ◽  
J. Paul Woods ◽  
Dorothee Bienzle ◽  
Geoffrey A. Wood ◽  
Brenda Lynn Coomber
Keyword(s):  
B Cell ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cell Lymphoma ◽  
Canis Familiaris ◽  
B Cell Lymphoma ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
High Confidence
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