Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology

Shinzato, Chuya; Yasuoka, Yuki; Mungpakdee, Sutada; Arakaki, Nana; Fujie, Manabu; Nakajima, Yuichi; Satoh, Nori

doi:10.3389/fmars.2014.00011

Cited by 34 publications

(26 citation statements)

References 21 publications

(34 reference statements)

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“…Universal primer sets for 13 microsatellite loci, developed for the Genus Acropora (Shinzato et al. ), were used for amplification of alleles. Four loci (4546m2, 8499m4, 7203m5, and 11401m4) were amplified under the following conditions.…”

Section: Methodsmentioning

confidence: 99%

Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan

Zayasu

Nakajima

Sakai

et al. 2016

Ecology and Evolution

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To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in the Pacific, using 13 microsatellite markers to investigate 298 colonies from 15 locations across the Nansei Islands in southwestern Japan. Genetic diversity was not significant among sampling locations, even in possibly peripheral locations. In addition, our results showed that there are at least two populations of A. tenuis in the study area. The level of genetic differentiation between these populations was relatively low, but significant between many pairs of sampling locations. Directions of gene flow, which were estimated using a coalescence‐based approach, suggest that gene flow not only occurs from south to north, but also from north to south in various locations. Consequently, the Yaeyama Islands and the Amami Islands are potential northern and southern sources of corals. On the other hand, the Miyako Islands and west central Okinawa Island are potential sink populations. The Kerama Islands and the vicinity of Taketomi Island are potential contact points of genetic subdivision of coral populations in the Nansei Islands. We found that genetic population structure of A. tenuis in the Nansei Islands is more complex than previously thought. These cryptic populations are very important for preserving genetic diversity and should be maintained.

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Section: Methodsmentioning

confidence: 99%

Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan

Zayasu

Nakajima

Sakai

et al. 2016

Ecology and Evolution

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“…Due to the symbiont natural rates of increase, corals steadily release Symbiodinium cells into the surrounding environment (Yamashita et al, 2011), suggesting that close to reefs, seawater should contain detectable quantities of DNA from both corals and Symbiodinium. Recently, whole genome sequences of an Acropora coral (Shinzato et al, 2011) and Symbiodinium (Shoguchi et al, 2013;Lin et al, 2015;Aranda et al, 2016) have been published, and nextgeneration sequencing (NGS) technologies have been used to investigate coral reef biodiversity (Shinzato et al, 2014b(Shinzato et al, , 2015Combosch and Vollmer, 2015;Bongaerts et al, 2017). In the genus Symbiodinium, each clade contains multiple genetic types, and identification has been performed using ribosomal, mitochondrial, plastid, and nuclear DNA markers (Rowan and Powers, 1991;Wilcox, 1998;Lajeunesse, 2001;Santos et al, 2002;Takabayashi et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

et al. 2018

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Frequent, high-density coral monitoring is essential to understand coral reef ecosystems. For this purpose, we developed a novel method for simultaneous monitoring of Acropora corals and their symbiont, Symbiodinium, from environmental DNA (eDNA) in seawater using next generation sequencing technology (NGS). We performed a tank experiment with running seawater using 19 Acropora species. Complete mitochondrial genomes of all the Acropora species were assembled to create a database and major types of their Symbiodinium symbionts were identified. Then eDNA was isolated by filtering inlet and outlet seawater from the tanks. Acropora and Symbiodinium DNA were amplified by PCR and sequenced. We detected all of the tested Acropora types from eDNA samples. Proportions and numbers of DNA sequences were both positively correlated with masses of corals in the tanks. In this trial, we detected DNA sequences from as little as 0.04 kg of Acropora colony, suggesting that existence of at least one adult Acropora colony (∼30 cm diameter = 1 kg) per m 2 at depths <10 m could be detected using eDNA in the field. In addition, we detected major types of Symbiodinium within host corals from seawater, suggesting that it should be possible to detect major coral symbiont types if Acropora corals exist nearby, and possible free-living state Symbiodinium cells from eDNA in seawater. eDNA abundance of Symbiodinium types did not correlate well with frequencies of major Symbiodinium types in the corals, suggesting that quantification of Symbiodinium is difficult at this stage. Although this is the initial attempt to detect coral and Symbiodinium simultaneously from eDNA in seawater, this method may allow us to perform high-frequency, high-density coral reef monitoring of both corals and their symbionts in the near future.

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“…Paternity was determined using Acropora microsatellite marker 11745m3 ( [18], electronic supplementary material, figure S1b). DNA was extracted from larvae as follows: fixed larvae were treated with 20 ml lysis buffer (1 mg ml 21 proteinase K, 100 mM NaCl, 0.5% SDS, 10 mM EDTA and Tris-HCl pH 8.0) at 558C for 3 h, and then incubated at 988C for 5 min to terminate the reaction.…”

Section: (C) Sperm-choice Testmentioning

confidence: 99%

“…The resultant suspensions were used as templates for PCR. PCR was performed using GoTaq green mix (5.0 ml GoTaq, 3.6 ml water, 0.6 ml 10 mM microsatellite marker 11745m3 [18] and 0.2 ml template). The PCR protocol of Shinzato et al [18] was used, with some modifications.…”

Section: (C) Sperm-choice Testmentioning

confidence: 99%

“…PCR was performed using GoTaq green mix (5.0 ml GoTaq, 3.6 ml water, 0.6 ml 10 mM microsatellite marker 11745m3 [18] and 0.2 ml template). The PCR protocol of Shinzato et al [18] was used, with some modifications. The protocol was performed for 2 min at 958C, followed by 35 cycles of (948C for 30 s, 588C for 90 s and 728C for 1 min), and a final elongation at 608C for 30 min.…”

Section: (C) Sperm-choice Testmentioning

confidence: 99%

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The reef-building coral Acropora conditionally hybridize under sperm limitation

et al. 2016

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Multi-specific synchronous spawning risks both sperm limitation, which reduces fertilization success, and hybridization with other species. If available sperm of conspecifics are limited, hybridization with heterospecific sperm could be an alternative. Some species of the reef-building coral Acropora produce hybrid offspring in vitro , and therefore hybridization between such species does sometimes occur in nature. Here, we report that the interbreeding species Acropora florida and A. intermedia preferentially bred with conspecifics at optimal gamete concentrations (10 6 cells ml −1 ), but when sperm concentration was low (10 4 cells ml −1 ), A . florida eggs displayed an increased incidence of fertilization by sperm of A . intermedia . However, A . intermedia eggs never crossed with heterospecific sperm, regardless of gamete concentrations. It appears that A . florida eggs conditionally hybridize with heterospecific sperm; in nature, this would allow A . florida to cross with later-spawning species such as A . intermedia . These results indicate that hybridization between some Acropora species could occur in nature according to the number of available sperm, and the choice of heterospecific sperm for fertilization could be one of the fertilization strategies in the sperm-limited condition.

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Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology

Cited by 34 publications

References 21 publications

Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan

Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

The reef-building coral Acropora conditionally hybridize under sperm limitation

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