scholarly journals Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome

3 Biotech ◽  
2019 ◽  
Vol 9 (8) ◽  
Author(s):  
Yunsheng Wang ◽  
Muhammad Qasim Shahid ◽  
Fozia Ghouri ◽  
Sezai Ercişli ◽  
Faheem Shehzad Baloch
Keyword(s):  
Herbal Medicine ◽  
De Novo Assembly ◽  
De Novo ◽  
Snp Markers ◽  
Gastrodia Elata ◽  
Ssr And Snp Markers

scholarly journals Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 36
Author(s):  
Te-Hua Hsu ◽  
Yu-Ting Chiu ◽  
Hung-Tai Lee ◽  
Hong-Yi Gong ◽  
Chang-Wen Huang
Keyword(s):  
Molecular Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Growth Traits ◽  
Gene Diversity ◽  
Snp Markers ◽  
Cdna Libraries ◽  
Functional Markers ◽  
Genetic Management ◽  
Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

scholarly journals Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Wenlan Tian ◽  
Dev Paudel ◽  
Wagner Vendrame ◽  
Jianping Wang
Keyword(s):  
De Novo ◽  
Average Length ◽  
Snp Markers ◽  
Biodiesel Production ◽  
Kegg Database ◽  
Genomic Databases ◽  
Important Species ◽  
Biological Studies ◽  
Ssr And Snp Markers ◽  
De Novo Assembling

Jatropha (Jatropha curcasL.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.

De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers

2020 ◽  
Vol 58 (6) ◽  
pp. 914-934
Author(s):  
Yunsheng Wang ◽  
Muhammad Qasim Shahid ◽  
Fozia Ghouri ◽  
Faheem Shehzad Baloch
Keyword(s):  
Rna Sequencing ◽  
Ssr Markers ◽  
De Novo Assembly ◽  
De Novo ◽  
Gastrodia Elata

scholarly journals De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e102665 ◽  
Author(s):  
Camila Campos Mantello ◽  
Claudio Benicio Cardoso-Silva ◽  
Carla Cristina da Silva ◽  
Livia Moura de Souza ◽  
Erivaldo José Scaloppi Junior ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Hevea Brasiliensis ◽  
De Novo Assembly ◽  
De Novo ◽  
Rubber Tree ◽  
Snp Markers ◽  
Rubber Biosynthesis

scholarly journals Initial Steps of Photosystem II de Novo Assembly and Preloading with Manganese Take Place in Biogenesis Centers in Synechocystis

2012 ◽  
Vol 24 (2) ◽  
pp. 660-675 ◽  
Author(s):  
Anna Stengel ◽  
Irene L. Gügel ◽  
Daniel Hilger ◽  
Birgit Rengstl ◽  
Heinrich Jung ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
De Novo Assembly ◽  
De Novo

scholarly journals Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

2021 ◽  
Vol 18 (2) ◽  
pp. 170-175 ◽  
Author(s):  
Haoyu Cheng ◽  
Gregory T. Concepcion ◽  
Xiaowen Feng ◽  
Haowen Zhang ◽  
Heng Li
Keyword(s):  
De Novo Assembly ◽  
De Novo

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

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