Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species

White, Oliver W.; Doo, Bethany; Carine, Mark A.; Chapman, Mark A.

doi:10.3732/apps.1600050

Cited by 14 publications

(8 citation statements)

References 43 publications

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“…The density of eSSRs distribution was computed as one SSR per 17.75 kb in the present study and was higher than other species such as Argyranthemum brousonetii (2.3%, 27.00 kb) and Zingiber officinale (2.7%, 25.20 kb) (White et al, 2016;Awasthi et al, 2017), while it was lower than in some species such as Arachis hypogaea (17.7%, 3.30 kb), Curcuma longa (20.5%, 4.80 kb), and Curcuma alismatifolia (12.5%, 6.60 kb), respectively (Annadurai et al, 2013;Wang et al, 2018;Taheri et al, 2019). eSSR frequencies and their density in genomes may differ from species to species, because each species has different genetic construction.…”

Section: Identification Of Essrsmentioning

confidence: 46%

Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L.

et al. 2020

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In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atlı cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used in the assembly. The number of total contigs and unigenes was calculated as 98,831, and the length of N50 was 1,333 bp after assembly. A total of 14,308 dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide SSR motifs (4-17) were detected, and the most abundant SSR repeat types were trinucleotide (29.54%), dinucleotide (24.06%), hexanucleotide (20.67%), pentanucleotide (18.88%), and tetranucleotide (6.85%), respectively. Overall 250 primer pairs were designed randomly and tested in eight Pistacia species for amplification. Of them, 233 were generated polymerase chain reaction products in at least one of the Pistacia species. A total of 55 primer pairs that had amplifications in all tested Pistacia species were used to characterize 11 P. vera cultivars and 78 wild Pistacia genotypes belonging to nine Pistacia species (P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima, P. chinensis, P. terebinthus, P. palaestina, and P. lentiscus). A total of 434 alleles were generated from 55 polymorphic eSSR loci with an average of 7.89 alleles per locus. The mean number of effective allele was 3.40 per locus. Polymorphism information content was 0.61, whereas observed (Ho) and expected heterozygosity (He) values were 0.39 and 0.65, respectively. UPGMA (unweighted pair-group method with arithmetic averages) and STRUCTURE analysis divided 89 Pistacia genotypes into seven populations. The closest species to P. vera was P. khinjuk. P. eurycarpa was closer P. atlantica than P. khinjuk. P. atlantica-P. mutica and P. terebinthus-P. palaestina pairs of species were not clearly separated from each other, and they were suggested as the same species. The present study demonstrated that eSSR markers can be used in the characterization and phylogenetic analysis of Pistacia species and cultivars, as well as genetic linkage mapping and QTL (quantitative trait locus) analysis.

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Section: Identification Of Essrsmentioning

confidence: 46%

Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L.

et al. 2020

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“…Nuclear SSRs have been used successfully in studies investigating the origin of homoploid hybrid species (Liu et al., ; Sherman & Burke, ), and the nSSRs identified by White et al. () were effective in identifying genetic clusters for this study. The nSNP data set ( n = 4,736 SNPs) obtained by GBS was also informative for investigating the genetic distinctiveness of the hybrid species.…”

Section: Discussionmentioning

confidence: 99%

“…A combination of eight nuclear and four chloroplast SSR markers was used for population genetic analyses (Supporting Information ). The nuclear SSRs (nSSRs) were developed by White, Doo, Carine, and Chapman () and are known to be variable between the parental species A. broussonetii and A. frutescens . The chloroplast SSR (cpSSR) markers were developed by Bryan, McNicoll, Ramsay, Meyer, and De Jong () using Nicotiana tabacum L. but are universal for flowering plants.…”

Section: Methodsmentioning

confidence: 99%

Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum

et al. 2018

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Well‐characterized examples of homoploid hybrid speciation (HHS) are rare in nature, yet they offer the potential to study a number of evolutionary processes. In this study, we investigate putative homoploid hybrid species in the genus Argyranthemum (Asteraceae), a group of plants endemic to the Macaronesian archipelagos of the North Atlantic Ocean. We specifically address a number of knowledge gaps surrounding the origin(s) of A. sundingii and A. lemsii, which are thought to be derived from the same parental cross. Comparisons of leaf morphology suggest that A. sundingii and A. lemsii are distinct from their parental progenitors and distinguishable from each other based on leaf area. Ecological niche modelling (ENM) demonstrated that the homoploid hybrid species occupy novel habitats that are intermediate relative to the parental species. Nuclear simple sequence repeat markers (SSRs) and single nucleotide polymorphism (SNP) data indicate that the homoploid hybrid species are distinct from the parental taxa, while population‐level sampling of chloroplast SSRs and approximate Bayesian computation show that A. sundingii and A. lemsii are independently derived from the same parental cross. As such, Argyranthemum represents an example of independent homoploid hybrid speciation events with evidence of divergence in leaf morphology and adaptation to novel intermediate habitats. On oceanic islands, which are often typified by steep ecological gradients and inhabited by recently derived species with weak reproductive barriers, multiple HHS events from the same parental cross are not only possible but also likely to have played a more important role in oceanic island radiations than we currently think.

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“…Since the article by Sosa et al (2010) was published, the knowledge of genetic diversity measured with microsatellite markers in oceanic endemics has significantly increased ( Takayama et al, 2015 ; White et al, 2016 ; Yang et al, 2017 ). Therefore, we are now able to confirm that S. palmensis presents moderate levels of genetic diversity for a rare endemic ( Sosa et al, 2011 ).…”

Section: Discussionmentioning

confidence: 99%

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

Rodríguez-Rodríguez

Castro

Sosa

2018

PeerJ

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The translocation of individuals or the reinforcement of populations are measures in the genetic rescue of endangered species. Although it can be controversial to decide which and how many individuals must be reintroduced, populations can benefit from reinforcements. Sambucus palmensis is a critically endangered endemic to the Canary Islands. During the past 30 years, the Garajonay National Park (La Gomera) has carried out an intensive program of translocations using cuttings, due to the low germination rates of seeds. To assess the effect of the restorations on the population genetics of S. palmensis in La Gomera, we collected 402 samples from all the restored sites and all known natural individuals, which were genotyped with seven microsatellite markers. In addition, we conducted a species distribution modeling approach to assess how restorations fit the ecological niche of the species. Results show that there is a high proportion of clone specimens due to the propagation method, and the natural clonal reproduction of the species. Nonetheless, the observed heterozygosity has increased with the restorations and there still are private alleles and unique genotypes in the natural populations that have not been considered in the restorations. The population of Liria constitutes a very important genetic reservoir for the species. To optimize future reintroductions, we have proposed a list of specimens that are suitable for the extraction of seeds or cuttings in a greenhouse, as well as new suitable areas obtained by the species distribution models.

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Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species

Cited by 14 publications

References 43 publications

Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L.

Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L.

Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum

The restoration of the endangeredSambucus palmensisafter 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling

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