Stenotaphrum secundatum
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ABSTRACT:
PROVIDER: PRJNA684383 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Stenotaphrum secundatum Raw sequence reads
| PRJNA591244 | ENA
Project description:Stenotaphrum secundatum Diversity Panel raw sequence reads
| PRJNA1009420 | ENA
Project description:Stenotaphrum secundatum Diversity Panel raw sequence reads
| PRJNA1007876 | ENA
Project description:Stenotaphrum secundatum Genome sequencing and assembly v1a
| PRJNA980716 | ENA
Project description:Stenotaphrum secundatum PI410353 Genome sequencing and assembly v1a
| PRJNA1007755 | ENA
Project description:Stenotaphrum secundatum cultivar:Raleigh Genome sequencing and assembly
| PRJNA736077 | ENA
Project description:BACKGROUND:Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49?S. secundatum accessions. RESULTS:Based on seven types of phenotypic data, the 49?S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h =?0.47, I =?0.66) and ISSR markers (h =?0.45, I =?0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers. CONCLUSIONS:Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.
| S-EPMC7425169 | biostudies-literature
Project description:During ongoing DNA barcode (COI-5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C. secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2-3 spacer) to compare the Narragansett Bay C. secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C. secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.
| S-EPMC4662316 | biostudies-literature