Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Liu, Luxian; Jin, Xinjie; Chen, Nan; Li, Xian; Li, Pan; Fu, Chengxin

doi:10.1371/journal.pone.0139840

Cited by 14 publications

(20 citation statements)

References 59 publications

(64 reference statements)

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“…Despite the genetic distance among the genera, there were a sufficient number of shared loci recovered between the Zamiaceae and Cycadaceae genera. These results mirror what was found in Myricaceae (Liu et al, ) and Diapensiaceae (Hou et al, ), as they also found a significant drop in loci recovered in more distantly related taxa, indicating that genetic differences between families would be considerable, as we found between Zamiaceae and Cycadaceae.…”

Section: Discussionsupporting

confidence: 91%

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RADseq as a valuable tool for plants with large genomes—A case study in cycads

Clugston

Kenicer

Milne

et al. 2019

Molecular Ecology Resources

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Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60 Gbp. Restriction site‐associated DNA sequencing (RADseq) offers an approach to find genome‐wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high‐depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome‐wide markers.

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Section: Discussionsupporting

confidence: 91%

“…These results mirror what was found in Myricaceae (Liu et al, 2015) and Diapensiaceae (Hou et al, 2015), as they also found a significant drop in loci recovered in more distantly related taxa, indicating that genetic differences between families would be considerable, as we found between Zamiaceae and Cycadaceae.…”

Section: Assembly Of Radseq Datasupporting

confidence: 89%

RADseq as a valuable tool for plants with large genomes—A case study in cycads

Clugston

Kenicer

Milne

et al. 2019

Molecular Ecology Resources

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“…bangwei is the only semi-wild tea plant that has been reported [ 7 ] until now. Despite the relatively small population used in this study, the number of samples was comparable with those used in several molecular phylogenetic research papers focusing on Pedicularis [ 46 ], temperate bamboos [ 47 ] and Chinese bayberry [ 48 ] that used RAD-Seq technology. The methods for the identificaton of SNPs and genotyping were also similar to those used in these papers.…”

Section: Putative Selective Footprints During Tea Domesticationmentioning

confidence: 99%

“…Common to all of these approaches is the initial usage of restriction enzymes and subsequent sequencing of a small section of the genome to reduce the complexity of the target DNA. RAD-Seq, which was developed to identify polymorphic variants in genomic regions adjacent to restriction enzyme digestion sites [ 37 , 42 ], has proven to be particularly suitable for species that lack a published genome sequence [ 43 – 45 ] and has provided genome-scale SNP data that have successfully revealed information for phylogenetic inferences in Pedicularis [ 46 ], temperate bamboos [ 47 ] and Chinese bayberry [ 48 ], population genetics [ 49 – 50 ], species identification [ 51 – 52 ], species evolution [ 53 ] and phylogenomics [ 54 – 55 ]. Additionally, RAD-Seq can also be utilized for association mapping [ 56 ] and genetic mapping [ 42 , 57 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

et al. 2016

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Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.

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“…Rapid progress in high-throughput sequencing technologies has provided an opportunity to infer genome-wide information from organisms without reference genomes with affordable cost. Reduced-representation genome sequencing allows us to discover thousands of genetic markers from many samples for population genomics studies 17 – 19 . These methods which consisted of restriction site associated DNA sequencing (RAD-seq) and genotyping by sequencing (GBS) have been successfully applied to population genomics studies of mangy species 20 – 22 .…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq

Gao

Yin

et al. 2017

Sci Rep

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Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.

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Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Cited by 14 publications

References 59 publications

RADseq as a valuable tool for plants with large genomes—A case study in cycads

RADseq as a valuable tool for plants with large genomes—A case study in cycads

Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq

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