Mining and analysis of microsatellites in human coronavirus genomes using the in-house built Java pipeline

Umang, Umang,Bharti, Pawan Kumar,Husain, Akhtar Korea Genome Organization 2022 Genomics & informatics Vol.20 No.3

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

Simple Sequence Repeat (SSR) and GC Distribution in the Arabidopsis thaliana Genome

Mortimer Jennifer C,Batley Jacqueline,Love Christopher G,Logan Erica,Edwards David The Korean Society of Plant Biotechnology 2005 Plant molecular biology and biotechnology research Vol.7 No.1

We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the genome and a strong association within and around transcribed sequences, while G/C density is associated specifically with the coding portions of transcribed sequences. SSR motif repeat number shows a high degree of variation for each SSR type and a high degree of motif sequence bias reflecting local genome sequence composition. PCR primers suitable for the amplification of identified SSRs have been designed where possible, and are available for further studies.

Variable-number tandem repeat loci-discriminating <i>Pleurotus ostreatus</i> cultivars

Park, Bokyung,Ha, Byeong Seuk,Lee, Song Hee,Kim, Min-Keun,Choi, Jong In,Ryu, Jae-San Elsevier 2019 Mycoscience Vol.60 No.2

<P><B>Abstract</B></P> <P> <I>Pleurotus ostreatus</I> is one of the most important edible mushrooms. Many cultivars have been bred to meet consumer needs. The identification of cultivars based on the morphological characteristics is restricted because fruiting bodies are frequently capricious due to environmental conditions; accordingly, sequence-based methods are required. A total of 546 simple sequence repeat primers derived from the <I>P. ostreatus</I> genome were screened, and one primer, JHH_SSR-184, was found to show polymorphisms on the major cultivars in Korea. The sequences of the polymorphic loci showed variable-number tandem repeat loci-like features enabling cultivar specificity. Thus, these loci might be applicable to discriminate <I>P. ostreatus</I> cultivars.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The SSR marker discriminated the Korean major <I>Pleurotus ostreatus</I> cultivars. </LI> <LI> The cultivar specific sequences showed variable number tandem repeat loci-like feature. </LI> <LI> Nine loci with variable copy number of the repeat conferred the cultivar specificity. </LI> </UL> </P>

Isolation of New Microsatellite-containing Sequences in Acanthopanax senticosus

( Joon Ki Kim ),( Ki Wha Chung ) 한국식물학회 2007 Journal of Plant Biology Vol.50 No.5

Microsatellite markers, also called simple sequence repeats (SSRs), are comprised of a 2- to 6-nucleotide repeat motif. They are useful as molecular markers for genetic authentication, crop breeding programs, and linkage analysis for map-based cloning. From a microsatellite-enriched genomic library of Acanthopanax senticosus, we identified 239 new microsatellite-containing sequences. The di-nucleotide repeat units were the most abundant (55.2%), followed by tri-nucleotide repeat units (24.6%). In detailed repeat structures, the (AG)n motif was most frequent (30.5%), followed by the (AC)n motif (21.7%). Heptaand octa-nucleotide repeat motifs were found in each single locus, and a total of 33 (13.8%) complex repeat structures were recorded. This is the first report of mass isolation of microsatellites via screening of an A. senticosus library, and may well provide information useful as a genetic resource for the further study of A. senticosus.

Genetic Diversity and Population Structure of Asian Tomato Accessions Based on Simple-Sequence Repeats

( Sebastin Raveendar ),( Jong-wook Chung ),( Gi-an Lee ),( Jung-ro Lee ),( Kyung-jun Lee ),( Myoung-jae Shin ),( Yang-hee Cho ),( Kyung-ho Ma ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.3

Tomato (Solanum lycopersicum L.) is one of the most economically important plants in the family Solanaceae. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The objective of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall FST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.

Whole‐genome sequencing of north African honey bee Apis mellifera intermissa to assess its beneficial traits

Nizar Jamal Haddad,Noureddine ADJLANE,Deepti SAINI,Athul MENON,Venkatesh KRISHNAMURTHY,Devan JONKLAAS,J. Paul TOMKINS,Wahida LOUCIF-AYAD,Lisa HORTH 한국곤충학회 2018 Entomological Research Vol.48 No.3

Apis mellifera intermissa is the native honey bee subspecies of Algeria, and approximates a position among bee races between tropical African and European breeds. This bee is very aggressive, nervous, and produces many broods with many queen cells. It is prone to swarming and exhibits defensive behavior and an abundant use of propolis. In the present study, pure line samples of A. m. intermissa collected from Blida (Algeria; 36°31′N, 2°58′E) with preferable Varroa resistance confirmed their through hygienic cleaning behavior and high temperature adaptation, were selected as a reference sample for full‐genome sequencing. Array comparative genomic hybridization (aCGH) was also performed on the same samples to validate genomic variations. These analyses will be an important source of information for the honey bee research community worldwide. The 240‐Mb genome was annotated with 26 355 transcripts and analyzed. Analysis of 133 pathways indicated an abundance of pathways related to metabolic processes, the biosynthesis of secondary metabolites, and biodegradation of xenobiotics . In addition to simple sequence repeat markers, variant analysis for beneficial trait genes, transposons, and phylogeny was performed. The mitochondrial genome and genes involved in immunity and chemoreception were identified and compared with those from other sequenced insect models. The indels obtained by sequencing were validated by aCGH. The genome sequence, annotation, and analysis of A. m. intermissa provides new understanding of the function of bee genes, and comparison with the genome of other A. mellifera subspecies promises to yield insights into the evolution of the adaptations to high temperature and resistance to Varroa parasite infestation.

Multiplex STS-SSR 마커를 활용한 국산밀 품종 판별

최리,유진희,홍수민,김경민,정한용,모영준,박철수 한국육종학회 2022 한국육종학회지 Vol.54 No.2

This study aimed to develop an agarose gel-based multiplex PCR assay using sequence-tagged site (STS) and simple sequencerepeat (SSR) markers that can differentiate Korean wheat cultivars. Forty-nine Korean wheat cultivars were primarily classified based on seedcoat color into red (36) and white (13) groups. Red wheat cultivars were further differentiated by three multiplex PCRs using molecular markersfor Ppo-A1/Vrn-D1a/Rht-B1b, Glu-A3ac/TaCwi-A1b/Lr34, and Glu-A1ac/Glu-B1b/KWSM003/TaSE96. Similarly, white wheat cultivars werefurther differentiated using two multiplex PCRs using the molecular markers for Ppo-A1/Vrn-D1a/Pina-D1a and Ppo-B1/Glu-B3h. A multiplexPCR assay using molecular markers for Glu-A1b/Glu-D1d/Wx-B1 was developed to differentiate four Korean wheat cultivars used as governmentcertified seeds: Baekkang, Hwanggeumal, Keumkang, and Saekeumkang. A multiplex PCR assay using molecular markers for Glu-B3h andPin-D1a was used for colored wheat cultivars, Arijinheuk, Ariheuk, and Chinese colored wheat. The multiplex PCR assays developed in thisstudy can provide useful molecular tools for differentiating Korean wheat cultivars, developing wheat seed management systems, and guaranteeingwheat seeds in Korea.

RNA Sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle Cybister chinensis (= Cybister japonicus) using the Illumina platform

황희주,Bharat Bhusan PATNAIK,강세원,박소영,정종민,상민규,박지은,민혜린,성지연,조용훈,노미영,이종대,정기윤,박홍석,정헌천,이용석 한국곤충학회 2018 Entomological Research Vol.48 No.1

Cybister chinensis Motschulsky, 1854 (synonym Cybister japonicus Sharp, 1873) is a beetle found in ponds and irrigation canals near rice fields regulating the aquatic faunal community through predation. However, due to loss of natural habitats, use of pesticides, and invasion of alien species the beetle is threatened. With lack of understanding at the trophic ecology and genomics level, the conservation study is hindered to a larger extent. In the present study, Illumina HiSeq 4000 platform has been used to unravel the whole‐larval transcriptome of the beetle. A total of 20,129 non‐redundant unigenes were assembled from 67,260,666 clean read sequences. About 18,743 unigenes found a homologous match in any one of the databases like PANM, UniGene, Swiss‐Prot, Clusters of Orthologous Groups (COG), Gene Ontology (GO), KEGG, and InterProScan. While the zinc finger domains topped the unigene hits, about 660 enzymes (2695 sequences) participating in metabolism, environmental information processing, genetic information processing and organismal system pathways were recorded. Furthermore, the HSP70 class, Toll‐like receptors 4, insulin‐receptor substrate, and AMP activated protein kinase showed conspicuous presence in the larval transcriptome. Out of a total of 12,491 unigene sequences examined, 1968 SSRs were detected. Majority of them were dinucleotide repeats with six iterations followed by trinucleotide and tetranucleotide repeats with five and four iterations, respectively. This is the first report of cDNA resources from C. japonicus till date. The data would be crucial for the assessment of the beetle in the wild and making an inventory for utilisation in future genomics and ecological studies.

The discrimination of domestic silkworm strains using simple-sequence loci

Kee-Young Kim,I-Yoen Jung,Yong-Soon Kim,Kang-Sun Ryu,Iksoo Kim,Byung-Rae Jin,Sang-Mong Lee,Pil-Don Kang 한국응용곤충학회 2008 한국응용곤충학회 학술대회논문집 Vol.2008 No.10

DNA-based technology are about to revolutionize the analysis of population structures as well as the determination of individual indentities. Furthermore, the analysis of polymorphic DNA regions make it possible to reach detailed conclusions on family relationships of individual. Microsatellite loci are increasingly used in population genetic and evolutionary studies. Simple sequence repeats (SSRs) or microsatellites consisted of short tandem repeats (usually 1-6 nucleotide) have shown advantages over other markers. We report here the isolation and characterization of nine highly polymerphic microsatellite loci for phylogenetic and population genetic use in silkworm. Comparative analysis of diverse silkworm strains with microsatellite locus revealed several alleles and discriminative heterozygosity values. A list of primer sequences that tag each locus is provided. The usefulness of microsatellite markers can be expected to enhance the classification in silkworm.

Evaluation of Genetic Diversity among Soybean Genotypes Using SSR and SNP

P. Tanya,P. Srinives,T. Toojinda,A. Vanavichit,Bo-Keun Ha,Jeong-Suk Bae,Jung-Kyung Moon,Suk-Ha Lee 韓國作物學會 2001 Korean journal of crop science Vol.46 No.4

Two different types of molecular markers, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), were used to measure genetic diversity among five Korean, eight Thai, and three wild soybeans. For SSR analysis, a total of 20 markers were surveyed to detect polymorphisms. For SNP analysis, four primers were designed from consensus sequence regions on disease resistance protein homolog genes, and used to amplify the genomic region. The PCR products were sequenced. A number of polymorphic SSR and SNP bands were scored on all genotypes and their genetic similarity was measured. Clustering analysis was performed independently on both types of markers. Clustering based on SSR markers separated the genotypes into three main groups originated from Korea, Thailand, and wild soybeans. On the other hand, two main groups were classified using SNP analysis. It seemed that SSR was more informative than SNP in this study. This may be due to the fact that SNP was surveyed on the smaller genomic region than SSR. Grouping based on the combined data of both markers revealed similar results to that of SNP rather than that of SSR. This might be due to the fact that more loci from SNP were considered to measure genetic relatedness than those from the SSR.