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

Abstract 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 phylogene...

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Autores principales:	JiYoung Yang, Yu-Chung Chiang, Tsai-Wen Hsu, Seon-Hee Kim, Jae-Hong Pak, Seung-Chul Kim
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/60deeeb8e3cf43d9b628766bc78e60ea
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spelling	oai:doaj.org-article:60deeeb8e3cf43d9b628766bc78e60ea2021-12-02T14:12:10ZCharacterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan10.1038/s41598-020-80143-12045-2322https://doaj.org/article/60deeeb8e3cf43d9b628766bc78e60ea2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80143-1https://doaj.org/toc/2045-2322Abstract 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.JiYoung YangYu-Chung ChiangTsai-Wen HsuSeon-Hee KimJae-Hong PakSeung-Chul KimNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q JiYoung Yang Yu-Chung Chiang Tsai-Wen Hsu Seon-Hee Kim Jae-Hong Pak Seung-Chul Kim Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
description	Abstract 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.
format	article
author	JiYoung Yang Yu-Chung Chiang Tsai-Wen Hsu Seon-Hee Kim Jae-Hong Pak Seung-Chul Kim
author_facet	JiYoung Yang Yu-Chung Chiang Tsai-Wen Hsu Seon-Hee Kim Jae-Hong Pak Seung-Chul Kim
author_sort	JiYoung Yang
title	Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
title_short	Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
title_full	Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
title_fullStr	Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
title_full_unstemmed	Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan
title_sort	characterization and comparative analysis among plastome sequences of eight endemic rubus (rosaceae) species in taiwan
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/60deeeb8e3cf43d9b628766bc78e60ea
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Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

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