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Genetic relationships among Eriobotrya species revealed by genome-wide RAD sequence data.

ABSTRACT: Restriction site-associated DNA sequencing (RAD-seq) was used to illuminate the genetic relationships among Eriobotrya species. The raw data were filtered, and 221 million clean reads were used for further analysis. A total of 1,983,332 SNPs were obtained from 23 Eriobotrya species and two relative genera. We obtained similar results by neighbor-joining and maximum likelihood phylogenetic trees. All Eriobotrya plants grouped together into a big clade, and two out-groups clustered together into a single or separate clade. Chinese and Vietnam accessions were distributed throughout the dendrogram. There was nonsignificant correlation between genotype and geographical distance. However, clustering results were correlated with leaf size to some extent. The Eriobotrya species could be divided into following three groups based on leaf size and phylogenetic analysis: group A and group B comprised of small leaves with <10 cm length except E. stipularis (16.76 cm), and group C can be further divided into two subgroups, which contained medium-size leaves with a leaf length ranged from 10 to 20 cm and a leaf length bigger than 20 cm.

SUBMITTER: Yang X

PROVIDER: S-EPMC5395450 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Genetic relationships among Eriobotrya species revealed by genome-wide RAD sequence data.

Yang Xianghui X Najafabadi Samaneh Kazemiani SK Shahid Muhammad Qasim MQ Zhang Zhike Z Jing Yi Y Wei Weiling W Wu Jingcheng J Gao Yongshun Y Lin Shunquan S

Ecology and evolution 20170321 8

Restriction site-associated DNA sequencing (RAD-seq) was used to illuminate the genetic relationships among Eriobotrya species. The raw data were filtered, and 221 million clean reads were used for further analysis. A total of 1,983,332 SNPs were obtained from 23 Eriobotrya species and two relative genera. We obtained similar results by neighbor-joining and maximum likelihood phylogenetic trees. All Eriobotrya plants grouped together into a big clade, and two out-groups clus ...[more]

PMID: 28428875

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Project description:Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD)--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient numbers of orthologous restriction sites are retained across species.

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Genetic relationships among Eriobotrya species revealed by genome-wide RAD sequence data.

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Genetic relationships among <i>Eriobotrya</i> species revealed by genome-wide RAD sequence data.

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