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 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.

Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia

“…The ndhB gene had the highest number of potential editing sites (15), followed by rpoB (6 sites), ndhF (5 sites), and ndhD (4 sites) in all 12 Hosta plastomes. The number of editing sites in those genes agrees with the results of previous studies (e.g., [ 30 , 42 , 43 , 44 ]). In general, the most frequent RNA editing sites were found in ndhB and ndhD genes, but 12 Hosta species showed that the rpoB gene also had a high number of potential editing sites.…”

“…Several studies have previously reported the positive selection of the major functional genes throughout plastome evolution (e.g., [ 50 , 51 , 52 , 53 ]). Furthermore, the essential gene of a modulator of the photosynthetic rbcL gene under positive selection has been reported in eudicot lineages, such as Fragaria (Rosaceae, [ 49 ]), Rubus (Rosaceae [ 44 ]), Gossypium (Malvaceae [ 54 ]), Panax (Araliaceae [ 50 ]), and monocot lineage Poaceae grass after the C3-C4 photosynthetic transition [ 52 ]. The positive selection of functional genes during plastome evolution is related to adaptation to environmental changes such as temperature, drought, carbon dioxide concentration, photosynthetic rate, and ecological niche or coevolutionary processes [ 52 , 55 ].…”

Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae)

“…Most of these genes, which are associated with photosynthesis, are crucial and conserved in plants ( Liang et al., 2020 ); thus, no non-synonymous mutations were detected. Six genes ( accD , ndhJ , rbcL , rpoC2 , ycf1, and ycf2 ) often associated with photosynthesis and gene transcription possess at least one site under positive selection in Litsea ( Gao et al., 2019 ; Wang et al., 2021 ; Yang et al., 2021 ). The positive selection of rbcL gene, which encodes for the large subunit of RuBisCO, is fairly common in many land plants ( Wen et al., 2021 ).…”

“…In Ilex , high rates of positive selection on the rbcL gene are associated with hybridization and introgression ( Yao et al., 2019 ). The acetyl-CoA carboxylase subunit D gene accD , NADH oxidoreductase gene ndhJ and the transcription gene rpoC2 have been shown to be under positive selection pressure in several plant species ( Gao et al., 2019 ; Yang et al., 2021 ). The functions of ycf1 and ycf2 are largely unknown, but they are indispensable for plant cell survival ( Drescher et al., 2000 ).…”

A Review on Chromatography–Mass Spectrometry Applications on Anthocyanin and Ellagitannin Metabolites of Blackberries and Raspberries

“…It is speculated that (poly)phenol bioaccessibility from berries is greater compared to other fruits, owing to their higher abundance but lower content of other macromolecules, including indigestible carbohydrates and proteins [ 7 ]. The genus Rubus L. constitutes a highly diverse plant genus [ 8 ], with species such as Rubus fruticosus (blackberry) and Rubus idaeus (raspberry) having a high polyphenolic content [ 9 , 10 , 11 ], and with compounds including anthocyanins, ellagitannins, and ellagic acid conjugates to be amongst the most prevalent (poly)phenols [ 9 , 11 , 12 , 13 ]. Anthocyanins in blackberries and raspberries are responsible for their characteristic pigmentation, with cyanidin 3-O-glucoside (C3G) being predominant in blackberries, whilst cyanidin 3-sophoroside in raspberries [ 2 , 9 , 14 , 15 , 16 ].…”