scholarly journals Development and validation of microsatellite markers from de novo transcriptome assembly of eggplant (Solanum melongena L.) and its putative progenitor S. incanum L. cultivars

2019 ◽  
Author(s):  
Shailesh K. Tiwari ◽  
Pallavi Mishra ◽  
Sakshi Singh ◽  
Vinay K Singh ◽  
Sarvesh P Kashyap ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Solanum Melongena ◽  
Biotic And Abiotic Stress ◽  
High Quality ◽  
Horticultural Traits ◽  
Parental Lines ◽  
Unique Genes

AbstractAn elite cultivar of eggplant, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.) with contrasting horticultural traits were used as parental lines to develop a mapping population of RILs. To accelerate breeding programs and to develop large scale SSR markers to be used in QTL mapping, RNASeq libraries from different tissues of both the parental plants were deep sequenced and assembled into representation of a high quality de novo transcriptome using Illumina-based Next Generation Sequencing technology. 99.99% of high quality bases were obtained from all the tissues and deposited in TSA database at the NCBI link. Total 3, 156 and 3, 196 SNVs were detected in S. melongena and S. incanum, respectively. In S. melongena, 11, 262 SSR while in S. incanum 11, 829 SSR containing regions were identified. Based on functional annotation, 21, 914 unique genes could be identified for S. melongena, 21,706 unique genes for S. incanum and overall, 60 different transcription factors were identified in both the lines. Further, a total of 536 SSR markers were designed and screened for polymorphism of which, 157 markers produced polymorphism between the parental lines. The polymorphic SSRs shall be used for genotyping of RILs to map QTLs for various horticultural traits in eggplant and identification of candidate genes in response to biotic and abiotic stress.

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.

De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae)

3 Biotech ◽  
2021 ◽  
Vol 11 (9) ◽  
Author(s):  
Lingdan Wang ◽  
Riqing Zhang ◽  
Maolin Geng ◽  
Yufeng Qin ◽  
Hailong Liu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

scholarly journals High Quality de Novo Transcriptome Assembly of Croton tiglium

2018 ◽  
Vol 5 ◽  
Author(s):  
Markus Haak ◽  
Svenja Vinke ◽  
Willy Keller ◽  
Julian Droste ◽  
Christian Rückert ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
High Quality ◽  
Croton Tiglium

scholarly journals De Novo Transcriptome Assembly and Development of EST-SSR Markers for Pterocarpus Santalinus L. f. (Red sanders) , a Threatened and Endemic Timber Tree of India

2021 ◽  
Author(s):  
Sindhu Agastikumar ◽  
Maheswari Patturaj ◽  
Aghila Samji ◽  
Balasubramanian Aiyer ◽  
Aiswarya Munnusamy ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Transcriptome Assembly ◽  
In Situ Conservation ◽  
Timber Harvest ◽  
Eastern Ghats ◽  
Structure Identification ◽  
Peninsular India ◽  
Pterocarpus Santalinus ◽  
Red Sanders

Abstract The endemic and precious timber Pterocarpus santalinus L. f. (Red sanders) is a drought hardy tree species for conservation in peninsular India due to its high risk of illegal timber harvest. It is only found in Eastern Ghats of India, and has become threatened owing to overexploitation of its valuable timber. The development of genomic resources, particularly simple sequence repeat (SSR) markers, is essential for strict implementation of in situ conservation measures and application of DNA information based red sanders genetic resource management. However, a lack of genomic data and efficient molecular markers limit the study of its spatial and temporal population genetic structure, identification of diversity hotspots and tree improvement. The current study aims at comprehensive molecular characterization of red sanders and the somatic chromosome counts, flow cytometry and EST-SSR analyses. The results revealed that red sanders is diploid with 2n=20 and the 2C genome size was 0.7872 ± 0.0561pg for the first time in this species. A total of 3128 EST-SSRs were detected based on 25,854 de novo assembled unigenes from transcriptome data and primer sets designed for 1953 SSRs. Fifty-nine EST-SSR markers were evaluated for polymorphism in the natural populations of red sanders and 13 were found to be suitable for genetic analysis. Two major transcription factor families bHLH and ERF, responsible for abiotic stress and secondary metabolite synthesis were analysed which would provide the foundation for further research on production of medicinally important biocompounds.

scholarly journals InTransBo: An Integrative Transcript Library to Enable Genome-Free Systematic Exploration of Bougainvillea

2020 ◽  
Author(s):  
Qi Luo ◽  
Ziliang Chen ◽  
Tingting Xu ◽  
Dangzheng Huang ◽  
Haitao Hou ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Information ◽  
Protein Coding ◽  
Traditional Medicines ◽  
Systematic Exploration ◽  
Genomic Resource ◽  
Better Than ◽  
Complete Genomic

Abstract Members of the genus Bougainvillea are rich sources of natural dyes, pigments, and traditional medicines. They are also commonly used as ornamentals in roadside landscape construction. However, the horticultural development of Bougainvillea flowers with extended growth periods and coloration is not always feasible. One reason is limited molecular knowledge and no genomic information for Bougainvillea. Here, we compiled an expressed transcript sequence library for Bougainvillea by integrating 20 Illumina-sequencing RNA transcriptomes. The library consisted of 97,623 distinct transcripts. Of these, 47,006 were protein-coding, 31,109 were lncRNA, and 19,508 were unannotated. We also confirmed that the library is an alternative genomic reference for accurate transcriptome assembly and its performance was substantially better than that of the de novo method. We also curated the Integrative Transcript Library database for Bougainvillea known as InTransBo (http://www.bio-add.org/InTransBo/index.jsp). To the best of our knowledge, the present study is the first large scale genomic resource for Bougainvillea. Overall, the library helps fill the genomic gap and elucidate the transcriptional nature of Bougainvillea. It may also advance progress in the precise regulation of flowering in horticulture. The same strategy can be readily applied toward the systematic exploration of other plant species lacking complete genomic information.

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