Population structure and genetic variation in the genus Dipteronia Oliv. (Aceraceae) endemic to China as revealed by cpSSR analysis

Yang, Jia; Li, S.; Sun, Genlou; Yuan, Yong–Ming; Zhao, Guifang

doi:10.1007/s00606-007-0641-z

Cited by 9 publications

(8 citation statements)

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“…Morphologically, the two genera obviously differ from each other in characters, such as the outline of samaras, the presence or absence of bud scales, the arrangement of leaves, and the chromosome number, while the two species of Dipteronia are very similar and distinguishable only on the basis of glabrous or hairy inflorescences, and sizes of leaves and nutlets. In AFLP-and cpSSR-based population genetic studies of the genus Dipteronia, we revealed a significantly high level of genetic differentiation between D. sinensis and D. dyerana; the two species shared no common cpSSR haplotype, and the same gene sequence evolved differently within each species (Yang et al 2007(Yang et al , 2008. In the present study, the placements of D. dyerana generated from the four plastid regions (trnL-F, psbM-trnD, trnD-trnT, and rpl16) were different.…”

Section: Discussionmentioning

confidence: 96%

“…In addition, the authors' former studies on Dipteronia showed that a significantly high level of genetic differentiation occurred between D. sinensis and D. dyerana ( F ST = 0.3904, F ST = 0.4424) by both amplified fragment length polymorphism (AFLP) and chloroplast simple sequence repeat (cpSSR) analyses, and no common haplotype was observed between D. sinensis and D. dyerana in cpSSR analysis (Yang et al 2007(Yang et al , 2008.…”

Section: Introductionmentioning

confidence: 95%

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What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Yang

Wang

et al. 2010

Plant Biosystems - An International Journal Dealing with all As

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DNA sequence data have been widely used to evaluate species delimitations and examine infraspecific relationships. However, species placements inferred from different nucleotide sequences are frequently in conflict. As an example of plant species placement based on nucleotide sequences, the phylogenetic placement of Dipteronia dyerana Henry (Aceraceae) was analyzed in the present study. The study species included eight Acer species (from different sections of Acer ), two Dipteronia species, and two outgroup taxa. Phylogenetic trees based on five datasets ( ITS , trnL-F , trnD-trnT , psbM-trnD , and rpl16 regions) as well as their combined datasets were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Further analyses were conducted to compare the strict consensus trees based on single regions and the combination of different regions. The results revealed a significant discrepancy among the phylogenetic placements of D. dyerana , inferred from various sequences. Phylogenetic trees using MP analysis based on trnD-trnT , rpl16 , and the four chloroplast combined sequences supported the genus Dipteronia as a monophyletic group, while in the other trees D. dyerana was positioned either in parallel with D. sinensis and Acer species or within the genus Acer . In ML analysis, only rpl16 and the four chloroplast combined sequence datasets supported the genus Dipteronia as a monophyletic group. We concluded that, although significant genetic differentiation occurred between D. dyerana and D. sinensis , D. dyerana was more advanced than D. sinensis . However, whether Dipteronia is monophyletic remains to be further investigated, e.g., by using more closely related taxa and more sequences. Furthermore, in addition to internal transcribed spacer sequences, more chloroplast gene sequences should be used for phylogenetic analyses of species.

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Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 95%

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Yang

Wang

et al. 2010

Plant Biosystems - An International Journal Dealing with all As

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“…As relic species of the Tertiary period, both species of Dipteronia have experienced long complex evolutionary histories to result in their current distributional status. Previous research based on analyses of chloroplast simple sequence repeats (cpSSRs) and amplified fragment length polymorphisms (AFLPs) revealed that significant genetic differences are present between D. sinensis and D. dyeriana ; these analyses also suggested that the populations of Dipteronia may have suffered a genetic bottleneck (Yang et al, 2007 , 2008 ). However, a clear understanding of the causes of their genetic divergence and speciation has still not been achieved; this is largely because of the lack of genomic resources.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

et al. 2016

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Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia.

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“…Furthermore, it is also meaningful to trace the evolutionary dynamics of these two tertiary relict plants. Previous studies of Dipteronia have focused on universal genetic markers, morphologic divergence and/or seed physical and chemical properties [5,6,7,8] and only few genetic diversity studies were analyzed based on AFLP and cpSSR [9,10]. However, studies on speciation, demographic history, genomic variation and adaptive divergence of Dipteronia were not widely conducted, possibly due to limited genomic resources and genetic markers.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)

Zhou

Bai

et al. 2016

Molecules

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Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.

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Population structure and genetic variation in the genus Dipteronia Oliv. (Aceraceae) endemic to China as revealed by cpSSR analysis

Cited by 9 publications

References 36 publications

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)

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