Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing

Yang, Yanci; Zhou, Tao; Qian, Zengqiang; Zhao, Guifang

doi:10.1016/j.ygeno.2021.03.013

Cited by 26 publications

(42 citation statements)

References 76 publications

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“…It was surprising, however, that the LSC region also contained variation, including 2577 bp differences among Juglandaceae plastomes, while SSC had 237 bp and IR had 296 bp differences among plastomes (Table 1 ). The identification of these regions of variability in protein-coding genes (CDS) and intergenic spacer (IGS) regions will be useful for the study of the evolution, phylogeny, biogeography of the walnut family (Juglandaceae) and Fagales [ 4 , 27 – 29 , 34 , 35 ] and, potentially, for DNA barcoding. Three potential pseudogenes ( infA , rpl22 , and ycf15 ) will also be valuable genetic resource for study of plastid transfer to the nucleus and for studies of the evolution of the walnut family and Fagales [ 10 , 20 ].…”

Section: Discussionmentioning

confidence: 99%

“…Phylogenomics applies genomic data to reconstruct the evolutionary biology of organisms [ 1 – 3 ], including the resolution of evolutionary relationships among and within family clades [ 4 – 7 ], genera, and closely related species [ 8 – 10 ]. Next generation sequencing (NGS) has made the generation of large-scale genomic data easier, cheaper, and greatly increased the availability complete chloroplast genomes [ 6 , 9 ] and whole genome resequencing data [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Next generation sequencing (NGS) has made the generation of large-scale genomic data easier, cheaper, and greatly increased the availability complete chloroplast genomes [ 6 , 9 ] and whole genome resequencing data [ 11 ]. The plastid genome has provided insight into molecular phylogeny and evolutionary relationships at many taxonomic levels [ 4 , 9 , 12 , 13 ]. Foundational genetic studies of the Juglandaceae were based on analysis of selected loci [ 14 – 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Zhou

Ebrahimi

et al. 2021

BMC Ecol Evo

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Background The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. Results We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. Conclusions A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Zhou

Ebrahimi

et al. 2021

BMC Ecol Evo

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“…The resolution of taxonomic ambiguities in problematic taxa also needs to focus on factors such as hybridization and polyploidization, as these can often cause identification failures (Hebert, Cywinska, et al, 2003; Yan et al, 2018). Incomplete lineage sorting and/or introgression among closely related taxonomic species, especially in Fagaceae (Fitzek et al, 2018; Yang et al, 2021), may also compromise the accurate identification of species severely. Therefore, the establishment of a reliable timber species barcode identification system will require further taxonomic and phylogenetic research to resolve species complexes, and it is vital that reference databases are updated regularly to keep pace with taxonomic revisions to reduce and correct misidentifications.…”

Section: Discussionmentioning

confidence: 99%

Assessing candidate DNA barcodes for Chinese and internationally traded timber species

Liu

et al. 2021

Molecular Ecology Resources

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Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH–psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH–psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family‐level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH–psbA+ITS2 are required to provide broader discrimination power. These newly‐generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.

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“… 2018 ; Yang et al. 2021 ). Till now, there are only 8 cp genomes have been published within this species abundant genus (Raubeson et al.…”

mentioning

confidence: 99%

The complete chloroplast genome of Ranunculus yunnanensis (Ranunculaceae)

Rao

Zeng

Du³

et al. 2021

Mitochondrial DNA Part B

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Ranunculus yunnanensis Franch is endemic in Yunnan and Sichuan Provinces, southwestern China. Here, we report the complete chloroplast (cp) genome of R. yunnanensis. The chloroplast genome is 156,050 bp in length, with 111 encoded genes, including 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. Maximum-likelihood phylogenetic reconstruction using the existing data of Ranunculus shows that R. yunnanensis is revealed at the basal position of the marsh buttercup clade. This result has improved a better understanding of the internal relationship of the Ranunculus .

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Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing

Cited by 26 publications

References 76 publications

Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Assessing candidate DNA barcodes for Chinese and internationally traded timber species

The complete chloroplast genome of Ranunculus yunnanensis (Ranunculaceae)

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