scholarly journals De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cuiping Zhang ◽  
Zhonglan Wu ◽  
Xinqiang Jiang ◽  
Wei Li ◽  
Yizeng Lu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Average Length ◽  
Resource Assessment ◽  
Sequence Information ◽  
Average Value ◽  
Information Index ◽  
Ssr Loci ◽  
Level Cluster ◽  
Polymorphism Level

AbstractStephanandra incisa is a wild-type shrub with beautiful leaves and white flowers and is commonly used as a garden decoration accessory. However, the limited availability of genomic data of S. incisa has restricted its breeding process. Here, we identified EST-SSR markers using de novo transcriptome sequencing. In this study, a transcriptome database containing 35,251 unigenes, having an average length of 985 bp, was obtained from S. incisa. From these unigene sequences, we identified 5,555 EST-SSRs, with a distribution density of one SSR per 1.60 kb. Dinucleotides (52.96%) were the most detected SSRs, followed by trinucleotides (34.64%). From the EST-SSR loci, we randomly selected 100 sites for designing primer and used the DNA of 60 samples to verify the polymorphism. The average value of the effective number of alleles (Ne), Shannon’s information index (I), and expective heterozygosity (He) was 1.969, 0.728, and 0.434, respectively. The polymorphism information content (PIC) value was in the range of 0.108 to 0.669, averaging 0.406, which represented a middle polymorphism level. Cluster analysis of S. incisa were also performed based on the obtained EST-SSR data in our work. As shown by structure analysis, 60 individuals could be classified into two groups. Thus, the identification of these novel EST-SSR markers provided valuable sequence information for analyzing the population structure, genetic diversity, and genetic resource assessment of S. incisa and other related species.

scholarly journals Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 411 ◽  
Author(s):  
Yu Ge ◽  
Lin Tan ◽  
Bin Wu ◽  
Tao Wang ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
High Throughput Sequencing ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Persea Americana ◽  
Illumina Hiseq ◽  
Ssr Loci ◽  
Ssr Development

Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.

Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou

2018 ◽  
Vol 16 (4) ◽  
pp. 306-314
Author(s):  
Chan Liu ◽  
Qing Tang ◽  
Chaohua Cheng ◽  
Ying Xu ◽  
Zemao Yang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
Trinucleotide Repeat ◽  
De Novo ◽  
Local Varieties ◽  
Genetic Studies ◽  
Oxidation Reduction ◽  
Ssr Loci ◽  
Wild Accessions ◽  
Expressed Sequence

AbstractChinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

scholarly journals Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

2018 ◽  
Vol 54 (No. 1) ◽  
pp. 17-25 ◽  
Author(s):  
D.-D. Vu ◽  
T.T.-X. Bui ◽  
T.H.-N. Nguyen ◽  
S.N.M. Shah ◽  
N.-H. Vu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Polymorphic Information Content ◽  
Shaanxi Province ◽  
Illumina Hiseq ◽  
Tissue Samples ◽  
Isolation And Characterization ◽  
Toxicodendron Vernicifluum

A total 20 074 230 sequencing reads were generated by Illumina HiSeq<sup>™ </sup>2500 from three different Toxicodendron vernicifluum tissue samples. In total, 48 693 unigenes with an average length of 703.34 bp were obtained by de novo assembly. 3392 potential EST-SSRs (expressed sequence tag-simple sequence repeat) were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 80 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 14 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism within the lacquer tree population in Langao, Shaanxi province, China. There were high genetic diversities (number of alleles per locus (A) = 2.93, polymorphic information content (PIC) = 0.53, observed heterozygosity (Ho) = 0.62 and expected heterozygosity (He) = 0.85) in the lacquer tree natural population. The four loci were significantly deviated from Hardy-Weinberg equilibrium. These results suggested high homozygosity in the population and low or deficiency in heterozygosity (inbreeding coefficient (Fis) = 0.27). These polymorphic EST-SSR markers will provide the base for further studies of genetic structure and breeding in T. vernicifluum.

Diversity, characterization and evaluation in Pummelo (Citrus maxima Merr.) cultivars using SSR markers and quality parameters

2019 ◽  
Vol 79 (3) ◽  
Author(s):  
Shahnawaz . Ahmed ◽  
H. S. Rattanpal ◽  
Gurteg . Singh
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Variability ◽  
Principal Component ◽  
Quality Parameters ◽  
Average Value ◽  
Low Genetic Diversity ◽  
Ssr Loci ◽  
Citrus Maxima ◽  
Maximum Heterozygosity

Fourteen pummelo (Citrus maxima Merr.) fruit varieties were evaluated through morphological and molecular methods to determine the genetic diversity among them. The analysis showed that maximum contribution (60%) towards diversity was due to the number of fruits per tree and rag percentage. Principal component analysis explained 80.26% of the total observed variability. Molecular characterization of pummelo varieties using 60 SSR markers revealed 26 polymorphic SSR loci having 77 amplified alleles and the number of alleles ranged from 1 to 4 with an average of 2.96 alleles per locus. The highest number of alleles per locus recorded was four as amplified by the SSR markers, CAT01, CS05, CCSM70, CIBE5156, AG14, CIBE4728 and CMS26. The PIC value ranged from 0.12 (CIBE5720) to 0.73 (CAT01) with average value of 0.53. Maximum heterozygosity was found in CAT01 (0.73) followed by CS05 (0.72) and AG14 (0.69). Pink Pummelo and White Pummelo showed the highest genetic similarity having coefficient of 89% and were closely related. The present study indicated low genetic diversity in pummelo varieties despite having high morphological variability, which could be elucidated by the fact that much of the phenotypic variation witnessed may be due to somatic mutations.

Molecular Profiling of Chilli Germplasm By Using SSR Marker

2021 ◽  
Vol 19 (1) ◽  
pp. 1-13
Author(s):  
MI Haque ◽  
S Ishtiaque ◽  
MM Islam ◽  
TA Mujahidi ◽  
MA Rahim
Keyword(s):  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Group Method ◽  
Arithmetic Means ◽  
Average Value ◽  
Pair Group ◽  
Index Matrix ◽  
Ssr Primers ◽  
Ssr Loci

The molecular characterization of chilli germplasm was done based on estimation of genetic diversity among the germplasm by using SSR markers. Forty chilli germplasms were analyzed using eight SSR primers. The SSR primers produced 30 SSR loci with an average value of 3.75 alleles per SSR locus. The similarity index matrix ranged from zero to 2.74. Polymorphic information content (PIC) of the SSR primers ranged from 0.543 to 0.735 with an average value of 0.658. The highest number (five) of allele was observed in primer CAMS-647, whereas the primers CAMS-864, CAMS-880 and CAMS-885 showed lowest number (three) of allele. The smallest allele was found in case of primer CAMS- 236 (176 bp), while the longest allele was detected for the primer CAMS- 864 (288 bp). Based on similarity matrix using the un-weighed Pair Group Method of Arithmetic Means (UPGMA) dendrogram, chilli germplasms were grouped into four main clusters. SSR markers showed genetic variability in the studied chilli germplasm.  SAARC J. Agric., 19(1): 1-13 (2021)

scholarly journals De novo Assembly and Characterization of the Testis Transcriptome and Development of EST-SSR Markers in the Cockroach Periplaneta americana

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Wan Chen ◽  
Yu-Xiang Liu ◽  
Guo-Fang Jiang
Keyword(s):  
Ssr Markers ◽  
Illumina Sequencing ◽  
Periplaneta Americana ◽  
De Novo ◽  
Average Length ◽  
Sequencing Technology ◽  
Reproductive Ability ◽  
Clusters Of Orthologous Groups ◽  
Similarity Searches

Abstract The cockroach Periplaneta americana is a notorious pest and threat to health worldwide, with a high reproductive ability. However, a limited amount of data is available on the developmental stage-specific transcriptomes of P. americana. To identify genes involved in developmental processes and to develop additional SSR markers in P. americana, we carried out de novo assembly of the P. americana transcriptome using Illumina sequencing. After removing low-quality sequences, we obtained 64,954,709 contigs, which were further assembled into 125,390 unigenes with an average length of 711 bp. Based on similarity searches against known proteins, we identified 48,300 unigenes based on a cut-off E-value of 10−5. The assembled sequences were annotated according to gene descriptions, gene ontology and clusters of orthologous groups. A total of 14,195 potential SSRs were identified and 41 of 63 randomly chosen primer pairs successfully amplified the predicted SSR markers, seven of which were polymorphic in size in P. americana. Furthermore, the Spag6 gene was confirmed to be testes specific and the fru and RPSA genes were related to the development of the testis. This is the special report of a P. americana transcriptome obtained using Illumina sequencing technology and a large number of molecular markers were developed.

scholarly journals Transcriptome analysis of colored calla lily (Zantedeschia rehmanniiEngl.) by Illumina sequencing:de novoassembly, annotation and EST-SSR marker development

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2378 ◽  
Author(s):  
Zunzheng Wei ◽  
Zhenzhen Sun ◽  
Binbin Cui ◽  
Qixiang Zhang ◽  
Min Xiong ◽  
...  
Keyword(s):  
Molecular Markers ◽  
De Novo ◽  
Average Length ◽  
Orthologous Group ◽  
Sequence Information ◽  
Nucleotide Polymorphisms ◽  
Protein Database ◽  
Illumina Hiseq ◽  
Significant Similarity ◽  
Calla Lily

Colored calla lily is the short name for the species or hybrids in sectionAestivaeof genusZantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here,de novotranscriptome sequencing was performed to produce large transcript sequences forZ. rehmanniicv. ‘Rehmannii’ using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genusZantedeschia.

scholarly journals De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 803
Author(s):  
Huapu Chen ◽  
Xiaomeng Li ◽  
Yaorong Wang ◽  
Chunhua Zhu ◽  
Hai Huang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Habitat Degradation ◽  
Betta Splendens ◽  
Orthologous Group ◽  
Functional Genes ◽  
Genetics Research ◽  
Ssr Loci ◽  
Paired End Sequencing ◽  
Eukaryotic Orthologous Group

The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

scholarly journals De novo transcriptome assembly, polymorphic SSR markers development and population genetics analyses for southern corn rust (Puccinia polysora)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiuyu Sun ◽  
Jie Liu ◽  
Keyu Zhang ◽  
Chong Huang ◽  
Leifu Li ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Molecular Genetic ◽  
Genotypic Diversity ◽  
Molecular Genetic Analysis ◽  
Significant Similarity ◽  
Southern Corn Rust ◽  
Puccinia Polysora

AbstractSouthern corn rust is a destructive maize disease caused by Puccinia polysora Underw that can lead to severe yield losses. However, genomic information and microsatellite markers are currently unavailable for this disease. In this study, we generated a total of 27,295,216 high-quality cDNA sequence reads using Illumina sequencing technology. These reads were assembled into 17,496 unigenes with an average length of 1015 bp. The functional annotation indicated that 8113 (46.37%), 1933 (11.04%) and 5516 (31.52%) unigenes showed significant similarity to known proteins in the NCBI Nr, Nt and Swiss-Prot databases, respectively. In addition, 2921 (16.70%) unigenes were assigned to KEGG database categories; 4218 (24.11%), to KOG database categories; and 6,603 (37.74%), to GO database categories. Furthermore, we identified 8,798 potential SSRs among 6653 unigenes. A total of 9 polymorphic SSR markers were developed to evaluate the genetic diversity and population structure of 96 isolates collected from Guangdong Province in China. Clonal reproduction of P. polysora in Guangdong was dominant. The YJ (Yangjiang) population had the highest genotypic diversity and the greatest number of the multilocus genotypes, followed by the HY (Heyuan), HZ (Huizhou) and XY (Xinyi) populations. These results provide valuable information for the molecular genetic analysis of P. polysora and related species.

scholarly journals Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6542 ◽  
Author(s):  
Shuheng Shen ◽  
Xutian Chai ◽  
Qiang Zhou ◽  
Dong Luo ◽  
Yanrong Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Genetic Studies ◽  
Onobrychis Viciifolia ◽  
Ssr Loci ◽  
Wild Accessions ◽  
High Level ◽  
Genetic Structures ◽  
Paired End Sequencing

Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

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