Identification and development of microsatellite (SSRs) makers of Exbucklandia (HAMAMELIDACEAE) by high-throughput sequencing

Huang, Cui‐Ying; Yin, Qianyi; Khadka, Dipak; Meng, Kaikai; Fan, Qingxia; Chen, Sufang; Liao, Wenbo

doi:10.1007/s11033-019-04800-z

Cited by 12 publications

(5 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent past revealed that the approach has been used to develop microsatellite markers in various species viz. S. leprosula (Ng et al 2009 ; Ng et al 2021 ), Grevillea thelemanniana (Hevroy et al 2013 ), Macadamia integrifolia (Nock et al 2016 ), Populus pruinosa (Yang et al 2017 ), G. juniperina (Damerval et al 2019 ), Exbucklandia tonkinensis (Huang et al 2019 ), etc., signifying the potential of this technology for the identification and development of novel SSRs in S. robusta , devoid of genome sequence information.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Mishra

Meena

Kant

et al. 2023

Funct Integr Genomics

View full text Add to dashboard Cite

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta . Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus ( N a), observed heterozygosity ( H o), expected heterozygosity ( H e), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae. Supplementary Information The online version contains supplementary material available at 10.1007/s10142-023-00975-8.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Mishra

Meena

Kant

et al. 2023

Funct Integr Genomics

View full text Add to dashboard Cite

show abstract

“…This approach has been recently used to develop microsatellite markers in various species, viz. G. thelemanniana (Hevroy et al 2013), Macadamia integrifolia (Nock et al 2016), Populus pruinosa (Yang et al 2017), G. juniperina (Damerval et al 2019), Exbucklandia tonkinensis (Huang et al 2019) and Salvadora oleoides (Bhandari et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta

Dabral

Shamoon

Meena

et al. 2021

Physiol Mol Biol Plants

View full text Add to dashboard Cite

“…Some genomic markers related to drug response were obtained from it, and they were applied to clinical treatment with success. The literature [ 6 ] researched that kinase inhibitors such as verofenib have clinical therapeutic effects on BRAF and EGFR mutations. Researchers utilised gene expression profile information from the literature [ 7 ].…”

Section: Related Workmentioning

confidence: 99%

Research on Cancer Molecular Typing Based on High-Throughput Sequencing Technology

Dan

2021

Computational and Mathematical Methods in Medicine

View full text Add to dashboard Cite

This paper studies the role of high-throughput measurement technology in cancer molecular typing. Based on the Dendrix algorithm, the model proposed in this paper selects the gene replication time as an inherent attribute that affects the frequency of gene mutations and adds it to the model. After setting the size of the gene set, compared with the Dendrix algorithm, the model does not need to delete the gene set that has been found in the process of searching the pathway, and it can find more driving pathway gene sets. Based on the high coverage and high exclusivity of the driving gene set in the pathway and the influence of gene covariates, this paper constructs an adaptive multiobjective optimization model. In order to overcome the problem of gene mutation heterogeneity, this model introduces gene covariates as the weight of gene mutation frequency so that the model is adaptive to each gene. The analysis of the research results shows the reliability of high-throughput sequencing technology.

show abstract

Identification and development of microsatellite (SSRs) makers of Exbucklandia (HAMAMELIDACEAE) by high-throughput sequencing

Cited by 12 publications

References 17 publications

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta

Research on Cancer Molecular Typing Based on High-Throughput Sequencing Technology

Contact Info

Product

Resources

About