Dataset Information

A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.

ABSTRACT: Premise:The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. Methods:We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes. Results:We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. Conclusions:Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.

SUBMITTER: Sanderson BJ

PROVIDER: S-EPMC7598885 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.

Sanderson Brian J BJ DiFazio Stephen P SP Cronk Quentin C B QCB Ma Tao T Olson Matthew S MS

Applications in plant sciences 20201025 10

<h4>Premise</h4>The family Salicaceae has proved taxonomically challenging, especially in the genus <i>Salix</i>, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.<h4>Methods</h4>We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes.<h4>Res ...[more]

PMID: 33163293

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Project description:BACKGROUND: Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains. RESULTS: DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function" and require further analysis. We also identified nine proteins common to both European domestic ruminants tested. CONCLUSION: Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored.

Dataset Information

A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.

Publications

A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.

Similar Datasets

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