Dataset Information

Twenty-seven low-copy nuclear primers for Lindera obtusiloba (Lauraceae): A Tertiary relict species in East Asia.

ABSTRACT:

Premise of the study

To investigate a more detailed evolutionary history of Lindera obtusiloba (Lauraceae) and other Lindera species, polymorphic low-copy nuclear primers were developed.

Methods and results

Unigenes of the L. obtusiloba transcriptome greater than 800 bp in length were randomly chosen for initial design of 168 primers. Agarose gel electrophoresis and Sanger sequencing were used to select low-copy nuclear genes. Twenty-seven primers were obtained and were used to investigate genetic diversity in 90 individuals from 24 populations. The nucleotide diversity ranged from 2.11 × 10^-3 to 8.99 × 10^-3, and haplotype diversity ranged from 0.57 to 0.97. These primers were also cross-amplified in L. aggregata, L. chunii, L. erythrocarpa, and L. glauca; up to 15 primers were successfully amplified in these related species.

Conclusions

This methodology is effective for development of low-copy nuclear primers. The 27 primers developed here will be useful for evolutionary studies of L. obtusiloba and other Lindera species.

SUBMITTER: Ye JW

PROVIDER: S-EPMC5749822 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Publications

Twenty-seven low-copy nuclear primers for <i>Lindera obtusiloba</i> (Lauraceae): A Tertiary relict species in East Asia.

Ye Jun-Wei JW Li Qin Q Tian Xiang-Yu XY Bao Lei L Wang Hong-Fang HF Ge Jian-Ping JP

Applications in plant sciences 20171221 12

<h4>Premise of the study</h4>To investigate a more detailed evolutionary history of <i>Lindera obtusiloba</i> (Lauraceae) and other <i>Lindera</i> species, polymorphic low-copy nuclear primers were developed.<h4>Methods and results</h4>Unigenes of the <i>L. obtusiloba</i> transcriptome greater than 800 bp in length were randomly chosen for initial design of 168 primers. Agarose gel electrophoresis and Sanger sequencing were used to select low-copy nuclear genes. Twenty-seven primers were obtaine ...[more]

PMID: 29299398

Similar Datasets

Project description:Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.