Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands

Cho, Myong-Suk; Kim, Seung‐Chul; Yang, Ji-Young; Crawford, Daniel J.; Stuessy, Tod F.; López-Sepúlveda, Patricio

doi:10.3389/fpls.2020.594272

Cited by 18 publications

(21 citation statements)

References 48 publications

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“…Meanwhile, Kim et al [30] compared 21 Artemisia (32 accessions) and suggested the markers accD and ycf1 may represent the potential markers to be tested for the whole Asteraceae. Recognition of these two markers seem to be line with several other studies on the genera in Asteraceae, where either one of both markers were observed in the suggestion list [31,32]. The marker ycf1 is included among the 19 divergent hotspots although it possesses a lower nucleotide diversity (Pi = 0.0004), imply the potential application of these markers over all species of Asteraceae.…”

Section: Discussionsupporting

confidence: 87%

“…Overall, narrow nucleotide diversities for C. chinense are observed (Table 2), likely because of comparative analyses was made within species that sampling differently from two localities. The highly divergent hotspots usually are identi ed between closer species [30,31,32]. Furthermore, the chloroplast genomes of same species were relatively conserved, exhibited in less remarkable polymorphism.…”

Section: Discussionmentioning

confidence: 99%

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Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae)

et al. 2021

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Crossostephium chinense is a traditional Chinese medicinal herb and it is often cultivated as an ornamental plant. Previous studies on this species mainly focused on its chemical composition and it was represented rarely and marginally in genetic studies, which limited knowledge about its genetic background, and thus genomic resources remain scarce. To develop both chloroplast and nuclear polymorphic microsatellites for C. chinense, potential microsatellites were screened from genome skimming data of two individuals of C. chinense. Sixty-four and 63 cpSSR markers were identi ed from two chloroplast genomes of C. chinense. This study performed for the rst-ever study on employment of genome skimming data and CandiSSR, consequently a total of 133 polymorphic nSSRs were developed. Ten nSSRs were randomly selected to test their transferability across 35 individuals from three populations of C. chinense, and 20 individuals each of Artemisia stolonifera and A. argyi. Cross-ampli cations were successful done for C. chinense, and were partially successful ampli ed for both Artemisia species. The number of alleles varied from two to nine. The observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 0.286 and from 0.029 to 0.755, respectively. These genomic resources will be valuable for population genetics and conservation studies in C. chinense and Artemisia.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae)

et al. 2021

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“…We, therefore, also restricted our use of the plastome to the protein-coding CDS and refrained from attempting to use the entire plastome, thus also including non-coding regions, for the phylogenetic analysis. This restriction must be seen as critical in the light of recently reported gene tree conflicts in phylogenies based on plastome data (e.g., Gonçalves et al, 2019 ; Walker et al, 2019 ; Cho et al, 2020 ; Köhler et al, 2020 ), which questions the assumption of the plastome as a single locus. Cho et al (2020) recovered different topologies for deep branches in Sonchus comparing phylogenetic reconstruction based on the protein-coding CDS only, with one based on the entire plastome, and Köhler et al (2020) even recorded conflicting topologies among major clades of Opuntioideae (Cactaceae), when exploring different assemblies of top-informative CDS markers.…”

Section: Discussionmentioning

confidence: 99%

“…This restriction must be seen as critical in the light of recently reported gene tree conflicts in phylogenies based on plastome data (e.g., Gonçalves et al, 2019 ; Walker et al, 2019 ; Cho et al, 2020 ; Köhler et al, 2020 ), which questions the assumption of the plastome as a single locus. Cho et al (2020) recovered different topologies for deep branches in Sonchus comparing phylogenetic reconstruction based on the protein-coding CDS only, with one based on the entire plastome, and Köhler et al (2020) even recorded conflicting topologies among major clades of Opuntioideae (Cactaceae), when exploring different assemblies of top-informative CDS markers. However, it cannot in all cases be excluded so far that non-biological causes are responsible for such conflicts.…”

Section: Discussionmentioning

confidence: 99%

New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

2022

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Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1–3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.

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“…Cladogenetic speciation is generally known to involve an initial immigrant population splitting into morphologically and ecologically distinct evolutionary lineages through adaptation to divergent habitats on the island, resulting in two or more new species being recognized taxonomically. There are numerous examples of this speciation mode, including the Lobelia complex (Campanulaceae) ( Givnish et al, 2009 ) and the silversword alliance ( Carlquist et al, 2003 ) in Hawaii; Scalesia (Asteraceae) in the Gálapagos Islands ( Eliasson, 1974 ; Schilling et al, 1994 ; Fernández-Mazuecos et al, 2020 ); Echium (Boraginaceae) ( Böhle et al, 1996 ; Garcıa-Maroto et al, 2009 ), Aeonium (Crassulaceae) ( Jorgensen and Olesen, 2001 ; Mort et al, 2002 ), and the woody Sonchus alliance (Asteraceae) ( Kim et al, 1996a , b , 2008 ; Santiago and Kim, 2009 ) in the Canary Islands; and Dendroseris and Robinsonia (Asteraceae) in the Juan Fernández Islands ( Crawford et al, 1998 ; Cho et al, 2020 ). In addition to the adaptive radiation in heterogeneous habitats, examples of cladogenetic speciation triggered by non-adaptive radiation have been also presented, such as Nigella arvensis complex (Ranunculaceae) in the Aegean Archipelago ( Comes et al, 2008 ; Jaros et al, 2018 ) and Helianthemum (Cistaceae) in the Canary Islands ( Albaladejo et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation

et al. 2021

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Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.

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Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands

Cited by 18 publications

References 48 publications

Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae)

Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae)

New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation

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