Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula

Yang, Ji-Young; Takayama, Kōji; Pak, Jae‐Hong; Kim, Seung‐Chul

doi:10.3390/genes10100774

Cited by 11 publications

(16 citation statements)

References 52 publications

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“…In addition, the non-coding regions were found to be more divergent and variable than the coding regions. As expected, these findings are consistent with the patterns observed in common angiosperms [ 44 , 47 , 49 , 60 , 61 ]. These six plastomes are highly conserved despite differences in estimated divergence times in the Late Cretaceous period, with the crown ages of Rosoideae and Amygdaloideae being estimated to be 75.78 million and 90.18 million years, respectively [ 10 ].…”

Section: Resultssupporting

confidence: 91%

“…The relative synonymous codon usage (RSCU) value was also similar to that in R. takesimensis . Consistent with the patterns detected in Rubus [ 60 ] and other angiosperms [ 61 ] and algal lineages [ 62 ], we found that codon usage in the P. dickinsii var. glabrata and S. insularis plastomes is biased toward a high RSCU value of U and A at the third codon position.…”

Section: Resultssupporting

confidence: 90%

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Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea

Yang

Kang²,

Pak

et al. 2020

IJMS

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Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.

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Section: Resultssupporting

confidence: 91%

Section: Resultssupporting

confidence: 90%

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea

Yang

Kang²,

Pak

et al. 2020

IJMS

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“…The eight plastomes of Taiwanese endemic Rubus contained 131 genes: 84 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. Compared with previously reported GC content of Rubus plastomes (37.1%) 35 – 39 , the overall GC content ranged from 37.0% ( R . glandulosopunctatus, R. rubroangustifolius, and R. taiwanicolus ) to 37.3% ( R. incanus, R. parviaralifolius, and R .…”

Section: Resultscontrasting

confidence: 75%

“…In addition, despite their representations from two subgenera ( Idaeobatus and Malachobatus ), the plastomes are highly conserved, with no structural variations or content rearrangements. Interestingly, the highly conserved group II intron of atpF gene was lost in all eight plastomes regardless of their subgeneric assignments, as we demonstrated previously in the case of R. boninensis, R. crataegifolius, R. takesimensis and R. trifidus 35 , 39 . Within the major lineages of the family Rosaceae 45 , we found the complete atpF gene in members of the newly circumscribed subfamily Amygdaloideae, such as Prunus (KP732472), Pyrus (HG737342, AP012207), and Malus (NC040170, NC031163).…”

Section: Discussionsupporting

confidence: 76%

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Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

Yang

Chiang

Hsu³

et al. 2021

Sci Rep

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Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.

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Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision

Huang

Chen

Hummer

et al. 2023

TAXON

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Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910–1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large‐scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para‐ or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

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Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula

Cited by 11 publications

References 52 publications

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea

Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision

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