Yaya Qu’s research while affiliated with Southwest Forestry University and other places

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Publications (4)


Fruits of six Caryodaphnopsis species (A: C. tonkinensis, B: C. henryi, C: C. malipoensis, D: C. sp. 1, E: C. sp. 2, F: C. sp. 3)
Gene maps of the Caryodaphnopsis henryi mitogenome (A) and chloroplast genome (B). The annotation of the genomes was performed using GeSeq. The genes that are drawn outside of the circle are transcribed clockwise, whereas those that are drawn inside the circle are transcribed counter clockwise
Number and distribution of long repeats (A) and SSRs (B) in mitogenome sequence of Caryodaphnopsis henryi
Homological sequences between mitogenome and plastome of C. henryi. The blue circular segment represents the mitogenome, the green circular segment represents the plastome, and the line represents the homologous fragment. Different colors in the inner circle represent gene density
Gene order in the mitogenomes of Hernandia nymphaeifolia, Magnolia biondii, and Caryodaphnopsis henryi. H. nymphaeifolia mitochondrial genes are shown on the left, C. henryi mitochondrial genes in the middle, and M. biondii mitochondrial genes on the right, with different colors signifying the relevant collinear sections

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Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)
  • Article
  • Full-text available

June 2024

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77 Reads

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1 Citation

BMC Plant Biology

Shiting Yang

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Yaya Qu

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Background Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known. Results Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively. Conclusions The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

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The ML phylogenetic tree for I. grandiflora based on other 21 species (11 in Lauraceae, 2 in Hernandiaceae, 1 in Monimiaceae, 6 in Calycanthaceae, and 1 in Magnoliaceae) plastid genomes; the complete plastome sequences were from Lauraceae Chloroplast Genome Database (https://lcgdb.wordpress.com/) (13 species those numbers ending with LAU) and NCBI (other 9 species).
The complete plastome sequence of Illigera grandiflora

July 2021

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41 Reads

Illigera grandiflora, a kind of traditional medicinal liana, belongs to the Illigera Blume of the Hernandiaceae. In this study, we reported the characteristics of complete plastome for I. grandiflora. Its total plastome was 156,138 bp in length, comprising a large single-copy region(LSC) of 84,931 bp, a small single-copy region (SSC) of 18,544 bp, and a pair of inverted repeat (IR) regions of 26,549 bp. The overall GC content was 39.16% (LSC, 37.77%; SSC, 33.89%; IR, 43.21%). The plastome encoded 134 genes, including 83 protein-coding genes, 42 transfer RNA genes, and 10 ribosomal RNA genes. The relationships in our phylogeny showed that the two Illigera species are located in the same clade, with Hernandia nymphaeifolia being the next sister group, followed by Wilkiea huegeliana.


The ML phylogenetic tree for I. celebica based on other 14 species (two in Cryptocarya, two in Endiandra, one in Eusideroxylon, one in Hernandia, one in Wilkiea, three in Calycanthus, two in Chimonanthus, and one in Idiospermum) chloroplast genomes.
The complete chloroplast genome sequence of Illigera celebica

June 2020

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49 Reads

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3 Citations

Illigera celebica is an evergreen woody vine that belongs to genus Illigera Bl in the family Hernandiaceae and has medicinal value. The complete chloroplast genome of I. celebica was sequenced to determine its phylogenetic location with respect to the other species under the Laurales. Its whole chloroplast genome is 156,123 bp in length, and comprises a large single-copy region (LSC, 84,913 bp), a small single-copy region (SSC,18,775 bp), and a pair of inverted repeats (IRs, 26,217 bp). The overall GC content is 39.2% (LSC, 37.8%; SSC, 33.9%; IR, 43.4%). Maximum likelihood phylogenetic analysise (TVM + F + R2 model) was conducted using 15 complete chloroplast genomes of Laurales, and the results confirmed that Hernandia nymphaeifolia and Wilkiea huegeliana were located in the same lineage.

Citations (3)


... Mitochondria are maternally inherited organelles that contain genetic information distinct from that of the nucleus. The study of mitochondrial phylogeny can reveal different evolutionary patterns compared to nuclear genome, which is significant for understanding hybridization and incomplete lineage sorting during species evolution [81,82]. The comparison of the mitogenome of V. diffusa with those of 23 species from the same order, along with 2 species from the Zygophyllaceae family as an outgroup, revealed that V. diffusa and species from the Salicaceae family were grouped together. ...

Reference:

Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa
Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BMC Plant Biology

... For the former, the variations recorded in comparison with the other two samples of M. vovidesii could be explained by the fact that this sample comes from a different population than the rest of M. vovidesii, or that it inhabits a different ecosystem, so these variations are a response to the habitat or simply related to the individual itself. However, variations in plastomes can be the result of many other causes, including random mutations or genetic drift (Cao et al. 2024;Chen et al. 2021;Dong et al. 2023;Du et al. 2022). ...

Comparative Genomics and Phylogenetic Analysis of Chloroplast Genomes of Asian Caryodaphnopsis Taxa (Lauraceae)
  • Citing Article
  • February 2024

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