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

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.

Download Full-text

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Bioscience Reports ◽

10.1042/bsr20192252 ◽

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.

Download Full-text

Genome survey of Zanthoxylum bungeanum and development of genomic-SSR markers in congeneric species

Bioscience Reports ◽

10.1042/bsr20201101 ◽

2020 ◽

Vol 40 (6) ◽

Author(s):

Jingmiao Li ◽

Siqiao Li ◽

Lijuan Kong ◽

Lihua Wang ◽

Anzhi Wei ◽

...

Keyword(s):

Ssr Markers ◽

Gc Content ◽

Repeat Sequence ◽

Pcr Analysis ◽

Minimum Length ◽

Dinucleotide Repeats ◽

Genome Survey ◽

Genomic Ssr ◽

Ssr Loci ◽

Zanthoxylum Bungeanum

Abstract Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.

Download Full-text

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

Chinese Journal of Oceanology and Limnology ◽

10.1007/s00343-016-5250-7 ◽

2015 ◽

Vol 35 (1) ◽

pp. 203-214 ◽

Cited By ~ 9

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

Download Full-text

Genome survey and identification of polymorphic microsatellites provide genomic information and molecular markers for the red crab Charybdis feriatus (Linnaeus, 1758) (Decapoda: Brachyura: Portunidae)

Journal of Crustacean Biology ◽

10.1093/jcbiol/ruz074 ◽

2019 ◽

Vol 40 (1) ◽

pp. 76-81 ◽

Cited By ~ 3

Author(s):

Shaobin Fang ◽

Renxie Wu ◽

Xi Shi ◽

Yin Zhang ◽

Mhd Ikhwanuddin ◽

...

Keyword(s):

Microsatellite Loci ◽

Gc Content ◽

Repeat Sequence ◽

Sequencing Platform ◽

Genome Survey ◽

Expected Heterozygosity ◽

Polymorphic Microsatellites ◽

Polymorphic Microsatellite ◽

Insight Into ◽

Illumina Sequencing Platform

Abstract We conducted a whole genome survey in the portunid crab Charybdis feriatus (Linnaeus, 1758) using Illumina sequencing platform and developed a set of polymorphic microsatellite loci. A total of 117.7 Gb of clean reads were generated, with 74× coverage of the estimated genome size of 1.4 Gb. The GC content, heterozygosity rate, and repeat sequence rate of the genome were estimated to be 40%, 1.1%, and 51%, respectively. A total of 3,779,209 microsatellites were identified from the genome. Sixty microsatellite loci were evaluated in a wild population of 40 individuals. As a result, 14 polymorphic microsatellite loci (23.3%) were obtained. The number of alleles (3 to 15), polymorphism information content (0.365 to 0.884), observed heterozygosity (0.050 to 0.975), and expected heterozygosity (0.450 to 0.907) per locus averaged 6.8, 0.652, 0.691, and 0.707, respectively. We show that the genome of C. feriatus has a high heterozygosity and repeat sequence rates, and provide a novel insight into the genome profile of marine crabs. The genetic markers developed in this study are potentially useful for studies on population dynamics and conservation genetics of C. feriatus and other species of brachyuran crabs.

Download Full-text

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

Scientific Reports ◽

10.1038/s41598-021-92781-0 ◽

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.

Download Full-text

Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing

Bioscience Reports ◽

10.1042/bsr20201295 ◽

2020 ◽

Vol 40 (11) ◽

Author(s):

Bingjie Chen ◽

Zhicheng Sun ◽

Fangrui Lou ◽

Tian-xiang Gao ◽

Na Song

Keyword(s):

Sequence Data ◽

Gc Content ◽

Dinucleotide Repeats ◽

Genome Survey ◽

Genome Wide ◽

Sequencing Method ◽

High Quality Sequence ◽

Repeat Rate ◽

Nucleotide Repeats ◽

Distribution Frequency

Abstract Acanthogobius ommaturus is one of the suitable species to study the genetic mechanism of adaptive evolution, but there are few reports on its genetics. In the present study, the genomic survey sequencing method was used to analyze the genome characters of A. ommaturus. A total of 50.50 G high-quality sequence data were obtained in the present study. From the 19-mer distribution frequency, the estimated genome size was 928.01 Mb. The calculated sequence repeat rate was about 38.31%, the heterozygosity was approximately 0.17%, and the GC% content was approximately 40.88%. Moreover, 475,724 simple sequence repeats (SSRs) were identified. Among them, dinucleotide repeats were the most (53.70% of the total SSRs), followed by tri- (35.36%), hexa- (4.59%), tetra- (4.57%) and penta- (1.77%) nucleotide repeats type. This is the first genome-wide feature of this species to be reported.

Download Full-text

Genome Survey of Misgurnus Anguillicaudatus to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Mitochondrial Genome

10.21203/rs.3.rs-767195/v1 ◽

2021 ◽

Author(s):

Guiyun Huang ◽

Jianmeng Cao ◽

Chen Chen ◽

Miao Wang ◽

Zhigang Liu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Microsatellite Loci ◽

Complete Mitochondrial Genome ◽

Gc Content ◽

Repeat Sequence ◽

Misgurnus Anguillicaudatus ◽

Population Genetic Analysis ◽

Next Generation Sequencing Technology ◽

Genome Survey ◽

A Genome

Abstract The dojo loach Misgurnus anguillicaudatus is an important economic species in Asia because of its nutritional value and broad environmental adaptability. Despite its economic importance, genomic data from M. anguillicaudatus was unavailable. In the present study, we conducted a genome survey of M. anguillicaudatus using next-generation sequencing technology. Its genome size was estimated to be 1105.97 Mb by using K-mer analysis, and its heterozygosity ratio, repeat sequence content, GC content were 1.45%, 58.98%, and 38.03%, respectively. A total of 376,357 microsatellite motifs were identified and mononucleotides, with a frequency of 42.57%, were the most frequently repeated motifs, followed by 40.83% dinucleotide, 7.49% trinucleotide, 8.09% tetranucleotide, and 0.91% pentanucleotide motifs. The AC/GT, AAT/ATT, and ACAG/CTGT repeats were the most abundant motifs among dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. Besides, a complete mitochondrial genome was sequenced. Based on the maximum likelihood and Bayesian inference analyses, M. anguillicaudatus in this study was the “introgressed” mitochondrial type. Furthermore, a total of 376,357 SSR motifs were detected from the genome survey assembly. Seventy microsatellite loci were randomly selected from these SSR loci to test polymorphic, of which, twenty microsatellite loci were assessed in 30 individuals from a wild population. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) per locus ranged from 7 to 19, 0.400 to 0.933, and 0.752 to 0.938, respectively. All twenty loci were highly informative (PIC > 0.700). Eight loci deviated from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). This is the first report of a genome survey in M. anguillicaudatus, and genome information, mitochondrial genome, and microsatellite markers will be valuable for further studies on population genetic analysis, natural resource conservation, and molecular marker-assisted selective breeding.

Download Full-text

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

10.1101/2020.07.08.193318 ◽

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.

Download Full-text