Isolation and characterization of 13 polymorphic microsatellites for the Hokkai Shrimp, Pandalus latirostris

Azuma, Noriko; Seki, Yuta; Kikkawa, Yoshiaki; Nakagawa, Tomoyuki; Iwata, Yoko; Sato, Taku; Munehara, Hiroyuki; Chiba, Susumu

doi:10.1007/s12686-011-9396-5

Cited by 4 publications

(4 citation statements)

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“…We tested the genetic differentiation between the NTK and NTR populations using neutral genetic markers. We randomly chose 40 individuals from NTK ones and 46 from the NTR ones collected at the sampling in 2010 and used 8 microsatellite markers ( Pal-1 , Pal-2 , Pal-3 , Pal-144 , Pal-203 , Pal-152 , Pal-178 , and Pal-216 ) that had been previously developed for this species to examine their genetic differentiation [51] . Genomic DNA was extracted from the legs of ethanol-fixed shrimp using the DNeasy Blood & Tissue Kit (Qiagen) DNA isolation protocol for animal tissue.…”

Section: Methodsmentioning

confidence: 99%

Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing

et al. 2011

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While the study of phenotypic variation is a central theme in evolutionary biology, the genetic approaches available to understanding this variation are usually limited because of a lack of genomic information in non-model organisms. This study explored the utility of next-generation sequencing (NGS) technologies for studying phenotypic variations between 2 populations of a non-model species, the Hokkai shrimp (Pandalus latirostris; Decapoda, Pandalidae). Before we performed transcriptome analyses using NGS, we examined the genetic and phenotypic differentiation between the populations. Analyses using microsatellite DNA markers suggested that these populations genetically differed from one another and that gene flow is restricted between them. Moreover, the results of our 4-year field observations indicated that the egg traits varied genetically between the populations. Using mRNA extracted from the ovaries of 5 females in each population of Hokkai shrimp, we then performed a transcriptome analysis of the 2 populations. A total of 13.66 gigabases (Gb) of 75-bp reads was obtained. Further, 58,804 and 33,548 contigs for the first and second population, respectively, and 47,467 contigs for both populations were produced by de novo assembly. We detected 552 sequences with the former approach and 702 sequences with the later one; both sets of sequences showed greater than twofold differences in the expression levels between the 2 populations. Twenty-nine sequences were found in both approaches and were considered to be differentially expressed genes. Among them, 9 sequences showed significant similarity to functional genes. The present study showed a de novo assembly approach for the transcriptome of a non-model species using only short-read sequence data, and provides a strategy for identifying sequences showing significantly different expression levels between populations.

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Section: Methodsmentioning

confidence: 99%

Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing

et al. 2011

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“…Genomic DNA was extracted from each ethanol‐fixed egg (1 × 2 mm per egg) and from a portion of the pleopod (2 × 10 mm) of the ethanol‐fixed mother and candidate fathers of the eggs using Chelex 100 (Bio‐Rad Laboratories) following the manufacturer's instructions. Eggs and potential parental samples were genotyped at 3–6 microsatellite loci— Pal1 , Pal2 , Pal3 , Pal147 , Pal152 and/or Pal216 —that were developed for Hokkai shrimp at our study site before starting the present study (Azuma et al, 2011). The primers were fluorescently labelled with 5FAM, HEX or TAMRA, and PCR amplifications were performed as described in Azuma et al (2011).…”

Section: Methodsmentioning

confidence: 99%

“…Eggs and potential parental samples were genotyped at 3–6 microsatellite loci— Pal1 , Pal2 , Pal3 , Pal147 , Pal152 and/or Pal216 —that were developed for Hokkai shrimp at our study site before starting the present study (Azuma et al, 2011). The primers were fluorescently labelled with 5FAM, HEX or TAMRA, and PCR amplifications were performed as described in Azuma et al (2011). The PCR products were sized using ABI 3730XL DNA Sequencer with the size standard GeneScan 500LIZ (Thermo Fisher Scientific), and allele size was checked using the software Peak Scanner (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

“…The PCR products were sized using ABI 3730XL DNA Sequencer with the size standard GeneScan 500LIZ (Thermo Fisher Scientific), and allele size was checked using the software Peak Scanner (Thermo Fisher Scientific). Other details of the characterisation of the microsatellites and PCR amplification are described in Azuma et al (2011).…”

Section: Genetic Diversity In a Clutchmentioning

confidence: 99%

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Mechanisms that can cause population decline under heavily skewed male‐biased adult sex ratios

Chiba

Iwamoto

Shimabukuro

et al. 2023

Journal of Animal Ecology

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While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female‐selective harvesting. We examined the effect of ASR on the spawning success of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population. We experimentally examined how male‐biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male‐biased ASR could trigger a decline of genetic diversity in a population. We show that ASR skewed by female‐selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.

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Genetic population structure of the Hokkai shrimp Pandalus latirostris Rathbun, 1902 (Decapoda: Caridea: Pandalidae) from Zostera seagrass beds in Hokkaido, Japan

Azuma

Chiba

2017

Journal of Crustacean Biology

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Isolation and characterization of 13 polymorphic microsatellites for the Hokkai Shrimp, Pandalus latirostris

Cited by 4 publications

References 9 publications

Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing

Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing

Mechanisms that can cause population decline under heavily skewed male‐biased adult sex ratios

Genetic population structure of the Hokkai shrimp Pandalus latirostris Rathbun, 1902 (Decapoda: Caridea: Pandalidae) from Zostera seagrass beds in Hokkaido, Japan

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