Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast isolation and next-generation sequencing

Kurokochi, Hiroyuki; Nurtjahjaningsih, I. L. G.; Sukartiningsih,; Tan, Engkong; Asakawa, Shuichi; Saito, Yoko; Ide, Yuji

doi:10.1007/s12686-015-0485-8

Cited by 8 publications

(6 citation statements)

References 11 publications

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“…In this study, we detected 21 chloroplast haplotypes from nine populations ( Table 1 and Figure 1) using our previously developed chloroplast DNA markers [9]. Previously, several studies have examined the genetic distribution of tropical woody species through the analysis of chloroplast haplotypes.…”

Section: Discussionmentioning

confidence: 99%

“…The extracted DNA was stored at 4 • C until further analysis. Six chloroplast DNA regions (Ez_Cp_01, Ez_Cp_05, Ez_Cp_07, Ez_Cp_09, Ez_Cp_11, and Ez_Cp_12; [9], see Supplementary S2) were amplified by PCR, as described in [10]. Finally, chloroplast DNA sequencing reactions were performed as described in [10], using an ABI 3100 Genetic Analyzer (Thermo Fisher Scientific K.K., Kanagawa, Japan).…”

Section: Dna Extraction and Chloroplast Dna Sequencingmentioning

confidence: 99%

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Genetic Structure of the Tropical Tree Eusideroxylon zwageri in Indonesia Revealed by Chloroplast DNA Phylogeography

Nurtjahjaningsih¹,

Sukartiningsih

Kurokochi

et al. 2017

Forests

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Eusideroxylon zwageri is a large tropical rainforest tree native to Indonesia, Malaysia, the Philippines, and Brunei. Because of its high economic value, illegal logging and overexploitation is threatening this species in several locations in Indonesia. In this study, in order to conserve genetic resources, we investigated the genetic structure of E. zwageri in Indonesia using chloroplast DNA sequencing. Eusideroxylon zwageri samples were collected from the Kalimantan (56 trees from seven populations) and Sumatra (16 trees from two populations) islands of Indonesia. Approximately 3137 bp of chloroplast DNA was sequenced for each tree. Twenty-one haplotypes were identified, of which six haplotypes were detected from two or three populations, whereas the other 15 haplotypes were detected from one population each. For each population, one to six haplotypes were detected, and phylogenetically closer haplotypes were detected within the same population. Although the haplotypes were roughly divided into two groups, geographically-close populations did not always have phylogenetically-close haplotypes. Our results suggest that in Indonesia, E. zwageri showed a high genetic diversity at the chloroplast DNA level, and populations within a population were derived from similar maternal lineages. Therefore, transplantation within a population may be a feasible option for E. zwageri conservation. However, transplantation among different populations should be conducted with careful consideration, because geographic distances are not always related to phylogenetic distances in E. zwageri.

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Section: Discussionmentioning

confidence: 99%

Section: Dna Extraction and Chloroplast Dna Sequencingmentioning

confidence: 99%

Genetic Structure of the Tropical Tree Eusideroxylon zwageri in Indonesia Revealed by Chloroplast DNA Phylogeography

Nurtjahjaningsih¹,

Sukartiningsih

Kurokochi

et al. 2017

Forests

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“…DNA fragments, approximately 200 bp in length, were sequenced using an Ion Proton TM Sequencer (Applied Biosystems, Waltham, MA, USA). The sequences were collected as described by Kurokochi et al [ 16 ] and Sugiura et al [ 17 ]. SSRs were derived using MISA software ( ); 15 regions were selected and Primer3Plus software [ 18 ] was used to design primers for these SSRs ( Supplementary 1 ).…”

Section: Methodsmentioning

confidence: 99%

Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers

Kurokochi

Zhang

Takeuchi

et al. 2017

JoF

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The annual yield of matsutake mushrooms (Tricholoma matsutake) has consistently decreased in Japan over the past few decades. We used 15 polymorphic and codominant simple sequence repeat (SSR) markers, developed using next-generation sequencing, to carry out genetic analyses of 10 populations in Nagano, Japan. Using the SSRs, we identified 223 genotypes, none of which was observed in more than one population. The mean expected heterozygosity and standardized allelic richness values were 0.67 and 4.05, respectively. Many alleles appeared in only one of the 10 populations; 34 of these private alleles were detected with a mean number per population of 3.4. The fixation index (FST) and standardized genetic differentiation (G′ST) values were 0.019 and 0.028, respectively. Analysis of molecular variance (AMOVA) showed that the contribution of among population, among genets within a population, and within genets variation to the total variation was 2.91%, 11.62%, and 85.47%, respectively, with genetic differentiation being detected for all sources. Twenty-eight of 45 pairwise FST values were significantly larger than zero, and no pattern of isolation by distance was detected among the 10 populations. Bayesian-based clustering did not show clear differences among populations. These results suggest that reestablishment of a colony would be best accomplished by transplantation within a field; if this is not possible, then transplantation from within several dozen kilometers will cause little damage to the original population genetic structure.

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“…PCR products were adjusted essentially in accordance with Ion 16S Metagenomics kit (Thermo Fisher Scientific), however, the number of cycles for amplifying the library was 30 in this study. The amplified DNAs were set to an IonPGM sequencer (Thermo Fisher Scientific) according to Kurokochi et al (2015).…”

Section: Soil Dna Extraction Pyrosequencing and Community Analysismentioning

confidence: 99%

Bioactive properties of streptomyces may affect the dominance of Tricholoma matsutake in shiro

et al. 2020

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Tricholoma matsutake is known to be the dominant fungal species in matsutake fruitbody neighboring (shiro) soil. To understand the mechanisms behind matsutake dominance, we studied the bacterial communities in matsutake dominant shiro soil and non-shiro soil, isolated the strains of Streptomyces from matsutake mycorrhizal root tips both from shiro soil and from the Pinus densiflora seedlings cultivated in shiro soil. Further, we investigated three Streptomyces spp. for their ability to inhibit fungal growth and Pinus densiflora seedling root elongation as well as two strains for their antifungal and antioxidative properties.Our results showed that Actinobacteria was the most abundant phylum in shiro soil. However, the differences in the Actinobacterial community composition (phylum or order level) between shiro and non-shiro soils were not significant, as indicated by PERMANOVA analyses. A genus belonging to Actinobacteria, Streptomyces, was present on the matsutake mycorrhizas, although in minority. The two antifungal assays revealed that the broths of three Streptomyces spp. had either inhibitory, neutral or promoting effects on the growth of different forest soil fungi as well as on the root elongation of the seedlings. The extracts of two strains, including one isolated from the P. densiflora seedlings, inhibited the growth of either pathogenic or ectomycorrhizal fungi. The effect depended on the medium used to cultivate the strains, but not the solvent used for the extraction. Two Streptomyces spp. showed antioxidant activity in one out of three assays used, in a ferric reducing antioxidant power assay. The observed properties seem to have several functions in matsutake shiro soil and they may contribute to the protection of the shiro area for T. matsutake dominance.

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Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast isolation and next-generation sequencing

Cited by 8 publications

References 11 publications

Genetic Structure of the Tropical Tree Eusideroxylon zwageri in Indonesia Revealed by Chloroplast DNA Phylogeography

Genetic Structure of the Tropical Tree Eusideroxylon zwageri in Indonesia Revealed by Chloroplast DNA Phylogeography

Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers

Bioactive properties of streptomyces may affect the dominance of Tricholoma matsutake in shiro

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