Evolutionary Divergence between Toona ciliata and Toona sinensis Assayed with Their Whole Genome Sequences

Wang, Xi; He, Zi-Han; L, Li; Lv, Yan-Wen; Hu, Xin‐Sheng

doi:10.3390/genes13101799

Cited by 8 publications

(6 citation statements)

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“…Note that the large interval of the estimates of divergent times (Figure 4) could arise from the use of a wide range of divergent times derived from TimeTree database for calibrations (Kumar et al, 2017). This was the same situation for estimating the divergent times between T. ciliata and T. sinensis (Wang, Xiao, He, Li, Lv, Hu, et al, 2022;Wang, Xiao, He, Li, Song, et al, 2022). The fossil records are still lacking for the species that are closely related to the Toona genus.…”

Section: Evolutionary Divergence Among Varietiesmentioning

confidence: 99%

“…Here, we reported the phylogenetic relationships and the genetic differentiation among sympatric varieties with both the whole chloroplast genome sequence and markers, and explored the conservation strategy of this endangered species. Analysis with nuclear genomes will be present in a separate study using our recent assembly of nuclear genome sequences of T. ciliata as the reference genome (Wang, Xiao, He, Li, Lv, et al., 2022 ; Wang, Xiao, He, Li, Song, et al., 2022 ). One reviewer suggested inclusion of nuclear data analyses, but it is more appropriate to present the nuclear part in a separate study to accompany this work since more extensive analyses are needed with the resequencing data of these varieties.…”

Section: Introductionmentioning

confidence: 99%

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Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Xiao,

Wang,

et al. 2023

Ecology and Evolution

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Toona ciliata is an endangered species due to over‐cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well‐mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL‐trnF) and showed that genetic differentiation was generally insignificant among varieties (Фst = 0%–5%). Purifying selection occurred in all protein‐coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein‐coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome‐based phylogeny did not support the morphology‐based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

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Section: Evolutionary Divergence Among Varietiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Xiao,

Wang,

et al. 2023

Ecology and Evolution

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“…This was similar with the expression pattern of PmFBPs in P. massoniana [ 18 ], while different from the expression pattern of HbcpFBPs in Hevea brasiliensis , with a higher expression level in bark than that in leaves [ 45 ]. The reason for the different tissue expression patterns of FBP gene may be caused by different plant species, as genomic differences are associated with differences in ecological adaptation [ 46 ]. The expression patterns of NcFBP4 and NcFBP5 were similar, except that the expression of NcFBP5 in green tissue was higher ( Figure 4 ), indicating that NcFBP5 may be chloroplast FBP, which was consistent with the previous evolutionary analysis ( Figure 5 ).…”

Section: Discussionmentioning

confidence: 99%

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Que

Liang

Song

et al. 2022

Genes

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Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) gene has been found to play a key role in plant photosynthesis, sugar accumulation and other growth processes. However, no systemic analysis of FBPs has been reported in N. cadamba. A total of six FBP genes were identifed and cloned based on the N. cadamba genome, and these FBP genes were sorted into four groups. The characteristics of the NcFBP gene family were analyzed such as phylogenetic relationships, gene structures, conserved motifs, and expression patterns. A cis-acting element related to circadian control was first found in the promoter region of FBP gene. Phylogenetic and quantitative real-time PCR analyses showed that NcFBP5 and NcFBP6 may be chloroplast type 1 FBP and cytoplasmic FBP, respectively. FBP proteins from N. cadamba and 22 other plant species were used for phylogenetic analyses, indicating that FBP family may have expanded during the evolution of algae to mosses and differentiated cpFBPase1 proteins in mosses. This work analyzes the internal relationship between the evolution and expression of the six NcFBPs, providing a scientific basis for the evolutionary pattern of plant FBPs, and promoting the functional studies of FBP genes.

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“…Analysis of the mating system scored by nuclear SSR markers indicated that the T. ciliata complex is predominantly outcrossing, with partial selfing and inbreeding [ 24 ]. Recent genome sequencing provides a useful reference for studying the phylogenetic relationship among varieties and for developing nuclear molecular markers for breeding [ 25 , 26 ]. All these studies provide a general picture of the genetic diversity and population structure of the T. ciliata complex, which serves as a valuable reference to the genetic conservation of this endangered species in China.…”

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers

Wang,

Hu,

et al. 2024

Genes

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Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and π = 0.0303 for the psbA-trnH fragment and h= 0.8999 and π = 0.0189 for the trnL-trnL fragment. Phylogenetic analysis supported the division of the natural distribution of T. ciliata complex into western and eastern regions. The genetic diversity was higher in the western region than in the eastern region, showing significant phylogeographic structure. Genetic differentiation among populations was moderate (Φst=42.87%), and the effects of isolation by distance (IBD) were significant. A neutrality test and mismatch distribution analysis indicated that the distribution of the T. ciliata complex generally did not expand, although a few local populations could likely expand after bottleneck effects. The overall results were complementary to and consolidated previous studies using mitochondrial and nuclear DNA markers. We finally discussed strategies for the genetic conservation of the T. ciliata complex.

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Evolutionary Divergence between Toona ciliata and Toona sinensis Assayed with Their Whole Genome Sequences

Cited by 8 publications

References 50 publications

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers

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