Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Jeon, Jihyeon; Kim, Seung‐Chul

doi:10.3390/genes10010023

Cited by 69 publications

(56 citation statements)

References 45 publications

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“…Another phenomenon observed in all six orders, is that SSC regions and LSC have higher divergence than IR regions, indicating the IR is more conserved than single copy sequences (Figure 3). This pattern is also been reported in other plants [24–26].…”

Section: Resultssupporting

confidence: 89%

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Shi

Han²,

Li³

et al. 2019

Preprint

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AbstractMangroves are main components of an ecosystem which connect land and ocean and is of significant ecological importance. They are found around the world and taxonomically distributed in 17 families. Until now there has been no evolutionary phylogenetic analyses on mangroves based on complete plastome sequences. In order to infer the relationship between mangroves and terrestrial plants at the molecular level, we generated chloroplast genomes of 14 mangrove species from eight families, spanning six orders: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, Thespesia populnea), Myrtales (Laguncularia racemose, Sonneratia ovata, Pemphis acidula), and Sapindales (Xylocarpus moluccensis). The whole-genome length of these chloroplasts is from 149kb to 168kb. They have a conserved structure, with two Inverted Repeat (IRa and IRb, ~25.8kb), a large single-copy region (LSC, ~89.0kb), a short single-copy (SSC, ~18.9kb) region, as well as ~130 genes (85 protein-coding, 37 tRNA, and 8 rRNA). The number of simple sequence repeats (SSRs) varied between mangrove species. Phylogenetic analysis using complete chloroplast genomes of 71 mangrove and land plants, confirmed the previously reported phylogeny within rosids, including the positioning of obscure families such as Linaceae within Malpighiales. Most mangrove chloroplast genes are conserved and we found six genes subjected to positive or neutral selection. Genomic comparison showed IR regions have lower divergence than other regions. Our study firstly reported several plastid genetic resource for mangroves, and the determined evolutionary locations as well as comparative analyses of these species provid insights into the mangrove genetic and phylogenetic research.

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Section: Resultssupporting

confidence: 89%

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Shi

Han²,

Li³

et al. 2019

Preprint

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“…3A), SSC presents the highest nucleotide diversity, followed by LSC. Unlike other studies of the nucleotide diversity of chloroplast genomes such as Dysphania (<0.03) (Kim et al, 2019b) and Chenopodium (with one highly variable region showing the highest peak in an IR region with pi = 0.07885) (Hong et al, 2017), Rosa (<0.02) (Jeon and Kim, 2019), and Symplocarpus (<0.03) (Kim et al, 2019a), there is a group of high peaks on the Viburnum chloroplast genomes (29,800 to 31,200 bp; denoted by the blue circle labeled as 1 in Fig. 3A).…”

Section: Nucleotide Diversity Among Six Viburnum Speciesmentioning

confidence: 76%

Comparative chloroplast genomics and phylogenetic analysis of the <i>Viburnum dilatatum</i> complex (Adoxaceae) in Korea

Park¹,

Xi²,

2020

Korean J. Pl. Taxon

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Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

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“…In recent years, a large number of plastid genomes have been revealed and compared for studying of taxonomy, evolution, breeding and conservation (Gruzdev et al, 2019a;Twyford & Ness, 2017;Zhong et al, 2019). The plastid genome of woody ornamental plant species such as Prunus (Cho, Yoon & Kim, 2018;Xue et al, 2019), Rosa (Jeon & Kim, 2019), Paeonia (Li, Guo & Zheng, 2018), Camellia (Li et al, 2019;Zhang et al, 2019), have also been established.…”

Section: Introductionmentioning

confidence: 99%

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

Guo

et al. 2020

PeerJ

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Background Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. Methods The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. Results The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.

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Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae)

Cited by 69 publications

References 45 publications

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Comparative chloroplast genomics and phylogenetic analysis of the <i>Viburnum dilatatum</i> complex (Adoxaceae) in Korea

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

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