Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

2015 ◽  
Vol 35 (1) ◽  
pp. 203-214 ◽  
Author(s):  
Xia Lu ◽  
Sheng Luan ◽  
Jie Kong ◽  
Longyang Hu ◽  
Yong Mao ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Marsupenaeus Japonicus ◽  
Genome Survey ◽  
Genome Wide ◽  
Genome Survey Sequencing

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

2021 ◽  
Author(s):  
Xin Peng ◽  
Zhende Yang ◽  
Lei Xu ◽  
Hantang Wang ◽  
Chunhui Guo ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Gc Content ◽  
Pcr Amplification ◽  
Repeat Sequence ◽  
Survey Analysis ◽  
Genome Survey ◽  
Fundamental Information ◽  
Genome Wide ◽  
Genomic Ssr ◽  
Batocera Horsfieldi

Abstract The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. 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 it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

scholarly journals Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jee Yun Hyun ◽  
Puneet Pandey ◽  
Kyung Seok Kim ◽  
Alvin Chon ◽  
Daecheol Jeong ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Domestic Cat ◽  
Apex Predators ◽  
Genetic Studies ◽  
Genome Survey ◽  
Genome Wide ◽  
Conservation Genetic ◽  
High Discriminatory Power ◽  
Transnational Trade ◽  
Pcr Conditions

AbstractBig cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to hunting, habitat loss, and illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 152 big cats, and were found polymorphic in most of the tested species. We propose a set of 12 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.

scholarly journals Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study

2020 ◽  
Author(s):  
Jee Yun Hyun ◽  
Puneet Pandey ◽  
Kyung Seok Kim ◽  
Alvin Chon ◽  
Daecheol Jeong ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Domestic Cat ◽  
Apex Predators ◽  
Eurasian Lynx ◽  
Genetic Studies ◽  
Genome Survey ◽  
Genome Wide ◽  
Conservation Genetic ◽  
High Discriminatory Power ◽  
Transnational Trade

AbstractBig cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 99 big cat individuals and 7 Eurasian lynx. The developed markers were polymorphic in most of the tested species. We propose a set of 15 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.

Genetic Enhancement in Mungbean (Vigna radiata) as Revealed by Genome-Wide Mapped Microsatellite Markers

2021 ◽  
Author(s):  
Aditya Pratap ◽  
Chandra Mohan Singh ◽  
Sanjeev Gupta ◽  
Ajeet Kumar Gupta ◽  
Revanappa S. Birader ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Vigna Radiata ◽  
Genetic Enhancement ◽  
Genome Wide

scholarly journals Genome wide screen identifies microsatellite markers associated with acute adverse effects following radiotherapy in cancer patients

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuichi Michikawa ◽  
Tomo Suga ◽  
Atsuko Ishikawa ◽  
Hideki Hayashi ◽  
Akira Oka ◽  
...  
Keyword(s):  
Adverse Effects ◽  
Microsatellite Markers ◽  
Cancer Patients ◽  
Genome Wide

To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?

2008 ◽  
Vol 17 (17) ◽  
pp. 3808-3817 ◽  
Author(s):  
ÜLO VÄLI ◽  
ANNIKA EINARSSON ◽  
LISETTE WAITS ◽  
HANS ELLEGREN
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Genome Wide

scholarly journals A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3186
Author(s):  
Eunkyung Choi ◽  
Sun Hee Kim ◽  
Seung Jae Lee ◽  
Euna Jo ◽  
Jinmu Kim ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Fish Species ◽  
Evolutionary Biology ◽  
Average Rate ◽  
Antarctic Fish ◽  
Error Rates ◽  
Repeat Motif ◽  
Sequencing Error ◽  
Genome Survey ◽  
Next Generation Sequencing Ngs

Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

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