Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus

2021 ◽  
Author(s):  
R. Zhao ◽  
Z. Lu ◽  
S. Cai ◽  
T. Gao ◽  
S. Xu
Keyword(s):  
Genetic Markers ◽  
Whole Genome ◽  
Genome Survey

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Whole Genome Survey of Copy Number Variation in the Spontaneously Hypertensive Rat

Hypertension ◽  
2010 ◽  
Vol 55 (5) ◽  
pp. 1231-1238 ◽  
Author(s):  
Fadi J. Charchar ◽  
Michael Kaiser ◽  
Andrew J. Bingham ◽  
Nina Fotinatos ◽  
Fahima Ahmady ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Spontaneously Hypertensive Rat ◽  
Whole Genome ◽  
Spontaneously Hypertensive ◽  
Genome Survey ◽  
Hypertensive Rat ◽  
Number Variation

Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1

Genomics ◽  
2020 ◽  
Vol 112 (6) ◽  
pp. 4742-4748
Author(s):  
Shengyong Xu ◽  
Hao Zhang ◽  
Tianxiang Gao
Keyword(s):  
Whole Genome ◽  
Male And Female ◽  
Genome Survey ◽  
Survey Analyses

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 Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Sheng-yong Xu ◽  
Na Song ◽  
Shi-jun Xiao ◽  
Tian-xiang Gao
Keyword(s):  
Microsatellite Markers ◽  
Gc Content ◽  
The Philippines ◽  
Whole Genome Sequence ◽  
Northwestern Pacific ◽  
Whole Genome ◽  
Survey Analysis ◽  
Genome Survey ◽  
Sebastiscus Marmoratus ◽  
Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

scholarly journals Prospects and pitfalls in whole genome association studies

2005 ◽  
Vol 360 (1460) ◽  
pp. 1589-1595 ◽  
Author(s):  
Robert W Lawrence ◽  
David M Evans ◽  
Lon R Cardon
Keyword(s):  
Genetic Variation ◽  
Genetic Markers ◽  
Complex Traits ◽  
Large Scale ◽  
Association Studies ◽  
Whole Genome ◽  
Common Genetic Variation ◽  
Close Attention ◽  
Genome Association ◽  
Whole Genome Association

Recent large-scale studies of common genetic variation throughout the human genome are making it feasible to conduct whole genome studies of genotype–phenotype associations. Such studies have the potential to uncover novel contributors to common complex traits and thus lead to insights into the aetiology of multifactorial phenotypes. Despite this promise, it is important to recognize that the availability of genetic markers and the ability to assay them at realistic cost does not guarantee success of this approach. There are a number of practical issues that require close attention, some forms of allelic architecture are not readily amenable to the association approach with even the most rigorous design, and doubtless new hurdles will emerge as the studies begin. Here we discuss the promise and current challenges of the whole genome approach, and raise some issues to consider in interpreting the results of the first whole genome studies.

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