Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae)

Meng, Kaikai; Chen, Sufang; Xu, Ke‐Wang; Zhou, Renchao; Li, Mingwan; Dhamala, Man Kumar; Liao, Wenbo; Fan, Qingxia

doi:10.1016/j.ympev.2021.107083

Cited by 41 publications

(38 citation statements)

References 90 publications

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“…However, some discrepancies between nuclear and chloroplast-based phylogenies are common in plants, including Rosaceae [3,12,25,26]. While not investigated in this study, the phylogenetic position of Aria, Chamaemespilus and Torminalis based on nuclear DNA sequences seems to be not fully resolved.…”

Section: Discussionmentioning

confidence: 73%

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp.

Ulaszewski

Jankowska-Wróblewska

Świło

et al. 2021

Plants

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Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.

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Section: Discussionmentioning

confidence: 73%

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp.

Ulaszewski

Jankowska-Wróblewska

Świło

et al. 2021

Plants

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“…Complete chloroplast genomes have been relatively more successful than short sequence fragments in resolving the relationships of many land plant clades at different taxonomic levels [ 20 – 22 ]. In general, land plant chloroplast genomes are relatively stable and contain four extremely evolutionarily conserved regions: a pair of inverted repeat regions (IRa and IRb), a large single-copy region (LSC), and a small single-copy region (SSC) [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships

Lee

Mao

et al. 2022

BMC Genomics

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Background Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. Results We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. Conclusion Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.

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“…The expanding cp genome database provides an important basis for determining evolutionary relationships [30,34]. Phylogenetic trees based on different data had slightly varied topologies, with trees based on the whole cp genome and CDS data having the same topology, and being more credible than trees based on the IR area and introns [35][36][37][38]. We found two similar topological structures with few changes based on the full cp genome and the protein-coding sequences of 23 selected species, with Neolitsea sericea and Actinodaphne obovate as outgroup species (Table S3, Fig 7).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Comparative Complete Chloroplast Genome of Nine Species in Litsea (Lauraceae) and Uncover Evolutionary Dynamic Patterns

Song

Chen

et al. 2021

Preprint

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Background: Litsea, Lauraceae, is a group of evergreen trees or shrubs that widely distributed in tropical and subtropical countries, such as Asia and America. Species in Litsea are spontaneously distributed at a maximum altitude of 2,700 m from sea level. Pants and its extractions from Litsea species cover a wide range of medicinal and industrial values. The aromatic oil extracted from Litsea is of great value with citral as its main component. At present, studies related to gene resources of Litsea are limited in the morphological analysis, while studies at the genetic level are insufficient. We therefore firstly assembled and annotated the complete chloroplast genome of nine species in Litsea, carried out a serious of comparative analysis, and completed the construction of phylogenetic tree within genus Litsea. Results: The genome length ranged from 152,051 to 152,717 bp. A total of 128 genes were identified, including 84 protein-coding genes, 36 rRNA genes and 8 tRNA genes. High consistency of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) revealed highly conserved chloroplast phenotypes in species within the genus Litsea. Changes in gene length and the present of pseudogene ycf1Ψ that caused by IR contraction and expansion were reported. The non-coding regions, especially atpF - atpH and ndhC - trnV-UAC presented high gene divergence. PsbJ - psbE regions showed remarkably high nucleotide diversity (Pi) values. Furthermore, we constructed two phylogenetic trees, demonstrating two dominant clades within genus Litsea. And the differences between trees constructed by full chloroplast (cp) genome and protein-coding genes were revealed. Conclusion: Overall, the evolutionary pattern of Litsea species regarding structural features, repeats sequences and variations presented high consistency. Valuable genomic resources and theoretical basis were also provided for further research of taxonomic discrepancies, molecular marker-assisted breeding and phylogenetic relationships of Litsea and other angiosperm species.

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Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae)

Cited by 41 publications

References 90 publications

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp.

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp.

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships

Comparative Complete Chloroplast Genome of Nine Species in Litsea (Lauraceae) and Uncover Evolutionary Dynamic Patterns

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