Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

Shinmura, Yoshimi; Wee, Alison K. S.; Takayama, Kōji; Asakawa, Takeshi; Yllano, Orlex B.; Salmo, Severino G.; Ardli, Erwin Riyanto; Tung, Nguyen Xuan; Malekal, Norhaslinda Binti; Onrizal, Onrizal; Meenakshisundaram, Sankararamasubramanian Halasya; Sungkaew, Sarawood; Nazre, M.; Adjie, Bayu; Soe, Khin; Oguri, Emiko; Murakami, Noriaki; Baba, Shigeyuki; Webb, Edward L.; Kajita, Tadashi

doi:10.1007/s12686-012-9650-5

Cited by 4 publications

(3 citation statements)

References 14 publications

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“…Eleven microsatellite markers for S. alba developed by [18] were selected based on their level of polymorphism and ease of multiplexing: SA102, SA103, SA105, SA106, SA108, SA110, SA112, SA113, SA115, SA117 and SA123. All loci were genotyped using fluorescent-labeled primers with the following dye-primer combinations-6-FAM: SA102, SA103, SA112 and SA11; VIC: SA105 and SA106; NED: SA108, SA110, SA117 and SA123; and PET: SA113.Polymerase chain reaction (PCR) was performed using Qiagen Multiplex PCR Kit (Qiagen, Hilden, Germany) in a final volume of 5 μL with 1 μL of DNA.…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

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Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

Wee

Teo

Chua

et al. 2017

Forests

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Patterns of genetic structure are essential for a comprehensive understanding of the evolution and biogeography of a species. Here, we investigated the genetic patterns of one of the most widespread and abundant mangrove species in the Indo-West Pacific, Sonneratia alba J. Sm., in order to gain insights into the ecological and evolutionary drivers of genetic structure in mangroves. We employed 11 nuclear microsatellite loci and two chloroplast regions to genotyped 25 S. alba populations. Our objectives were to (1) assess the level of genetic diversity and its geographic distribution; and (2) determine the genetic structure of the populations. Our results revealed significant genetic differentiation among populations. We detected a major genetic break between Indo-Malesia and Australasia, and further population subdivision within each oceanic region in these two major clusters. The phylogeographic patterns indicated a strong influence of vicariance, oceanic barriers and geographic distance on genetic structure. In addition, we found low genetic diversity and high genetic drift at range edge. This study advances the scope of mangrove biogeography by demonstrating a unique scenario whereby a widespread species has limited dispersal and high genetic divergence among populations.

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Section: Dna Extraction and Genotypingmentioning

confidence: 99%

“…Fragment length was assigned by the GENEMAPPER 4.1 software (Applied Biosystems, Foster City, CA, USA) using GeneScan-600 LIZ size standard. Genotype data of MY4 (Sabah) were obtained from a published primer note [18]. …”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

Wee

Teo

Chua

et al. 2017

Forests

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“…An important conceptual shift with the advent of NGs technologies is that the aforementioned classical statistics, and newer concepts such as the coalescent, can be visualized as continuous variables distributed across a genome (Hohenlohe et al 2011). A critical aspect of these dense data is that they exhibit correlation among measurements at neighboring genomic regions that result from linkage disequilibrium (slatkin 2008(slatkin , Pritchard et al 2010. The degree to which this autocorrelation itself changes along the genome reflects selection and recombination as well as other evolutionary forces (charlesworth et al 2009).…”

Section: Continues Opposite Pagementioning

confidence: 99%

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

Willette¹,

Allendorf²,

Barber³

et al. 2014

BMS

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The emerging field of next-generation sequencing (NGs) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in southeast Asia. The first Pan-Pacific Advanced studies Institute (PacAsI) entitled "Genomic Applications to Marine science and resource Management in southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGs in helping address the aforementioned challenges. Here we synthesize discussions held during the PacAsI to provide perspectives and guidance to help scientists new to NGs choose among the variety of available advanced genomic methodologies specifically for marine science questions.

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Development of 11 polymorphic microsatellite markers for Xylocarpus granatum (Meliaceae) using next-generation sequencing technology

Tomizawa

Shinmura

Wee

et al. 2013

Conservation Genet Resour

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Human impacts have seriously damaged mangroves, and conservation of mangroves will require information on local and regional population genetic structures. Here, we report the development and polymorphism of eleven novel microsatellite markers, developed using next-generation sequencing on 56 samples of widespread mangrove species Xylocarpus granatum (Meliaceae) from nine populations across the Indo-West Pacific region. All loci were found to be polymorphic, with the number of alleles per locus ranging from four to 19. In a population from Sabah (Malaysia), the mean observed and expected heterozygosity per locus was 0.59 and 0.58, respectively. No null allele, significant linkage disequilibrium or deviation from Hardy-Weinberg equilibrium was detected among all loci. The eleven markers developed can be valuable tools to conservation genetics of this species across its distributional range.

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Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

Cited by 4 publications

References 14 publications

Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

Development of 11 polymorphic microsatellite markers for Xylocarpus granatum (Meliaceae) using next-generation sequencing technology

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