Utilizing next generation sequencing to characterize microsatellite loci in a tropical aquatic plant species Cryptocoryne cordata var. cordata (Araceae)

Rosazlina, Rusly; Jacobsen, N. Kingo; Ørgaard, Marian; Othman, Ahmad Sofiman

doi:10.1016/j.bse.2015.06.033

Cited by 4 publications

(4 citation statements)

References 15 publications

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“…In recent years, generating transcriptome data through RNA sequencing have been successfully reported for SSR marker development in non-model plants with no reference genome as de novo sequencing [ 12 ]. Accordingly, microsatellite markers have several uses in marker-assisted selection (MAS), linkage mapping or quantitative trait loci (QTL) mapping, phylogenetic, positional cloning, genetic divergence appraisal, genotypic profiling, and so forth [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

et al. 2018

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Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

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Section: Introductionmentioning

confidence: 99%

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

et al. 2018

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“…since the middle of the 1970s we have been working with various aspects of Cryptocoryne: taxonomy (for an overview see Bastmeijer, 2016), morphology and pollination (Ørgaard & Jacobsen, 1998), cytology (Jacobsen, 1977a;arends et al, 1982), geographical distribution and habitat ecology via flora contributions (ipor et al, 2009;Jacobsen, 1985Jacobsen, , 1987li & Jacobsen, 2010;Jacobsen et al, 2012;othman et al, 2009), and molecular studies (othman, 1997;othman et al, 2009;ipor et al, 2010;Jacobsen et al, 2015a;rosazlina et al, 2015, rosazlina 2016rosazlina et al2017). We have undertaken a largescale hybridization programme, resulting in the production of more than 80 interspecific F 1 generations of which only a few have yet been published (ipor et al, 2015;Jacobsen, 1977bJacobsen, , 1981arosazlina, 2016;rosazlina et al 2017).…”

Section: Methodsmentioning

confidence: 99%

Hybrids and the Flora of Thailand revisited: Hybridization in the South-East Asian genus Cryptocoryne (Araceae)

Jacobsen

Bastmeijer²,

Bogner³

et al. 2016

Thai Forest Bull., Bot.

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The south-east asian genus Cryptocoryne has been shown to hybridize more frequently than expected. Data are presented on the known naturally occurring hybrids including information on their discovery, naming, and recognition as hybrids. Many artificial hybrids produced over the years indicate that there are only relatively few barriers to crossing. a heterosis effect is prevalent in many encountered Cryptocoryne hybrids. Vegetative propagation is clearly an advantage in the establishment of hybrid populations and also in detecting the hybrids, since inferior hybrids have disappeared naturally. our results on Cryptocoryne also suggest that when the south-east asian floras become as well-known as temperate ones, the number of natural hybrids will be similar to those presently known from temperate regions.

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“…The early difficulties in isolating sequences from microsatellites were circumvented with the use of next-generation sequencing (NGS). Indeed, thousands of microsatellite loci can now be identified from a single NGS run ( Tang et al, 2008 ; Boomer and Stow, 2010 ; Castoe et al, 2010 ; Rosazlina et al, 2015 ). However, the current techniques present difficulties regarding PCR calibration and the choice of informative microsatellites with high specificity.…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

et al. 2018

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Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.

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Utilizing next generation sequencing to characterize microsatellite loci in a tropical aquatic plant species Cryptocoryne cordata var. cordata (Araceae)

Cited by 4 publications

References 15 publications

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Hybrids and the Flora of Thailand revisited: Hybridization in the South-East Asian genus Cryptocoryne (Araceae)

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

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