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Start Over Author "Lopez, Lua" Topic endangered species
3 results on '"Lopez, Lua"'

2. A multi-faceted approach for assessing evolutionary significant conservation units in the endangered Omphalodes littoralis subsp. gallaecica (Boraginaceae).

Author

Lopez, Lua, Retuerto, Ruben, Roiloa, Sergio, Santiso, Xabier, and Barreiro, Rodolfo

Subjects
*ENDANGERED species, *BORAGINACEAE, *CONSERVATION biology, *BIOLOGICAL variation, *NON-coding DNA, *NUCLEOTIDE sequence
Abstract

Genetic diversity is now regarded as a key component of biodiversity and its assessment has become a frequent addition to conservation studies. However, due to practical limitations, most studies assess genetic variation using neutral markers while the variability of evolutionary relevant quantitative traits is typically overlooked. Here, we simultaneously assessed neutral and quantitative variation in an endangered plant to identify the mechanism behind their spatial arrangement and to propose conservation guidelines for maximizing mid- to long-term survival. Omphalodes littoralis subsp. gallaecica is a self-fertilizing therophyte with an extremely narrow and fragmented distribution. Regardless of the marker set (non-coding sequences of cpDNA or Amplified Fragment Length Polymorphism loci), the five extant populations of O. littoralis subsp. gallaecica showed minimal to none neutral genetic diversity and a lack of gene flow between them. Moreover, genetic structure was identical in samples collected on two consecutive years suggesting that the seed bank cannot buffer against genetic loss. High rates of self-fertilization together with a strongly fragmented distribution and recurrent bottlenecks seem the likely mechanisms that may have led to a dramatic loss of genetic variation in a classic scenario drawn by genetic drift. Despite the extremely narrow distribution range, reciprocal transplant experiments revealed that the populations differed in several quantitative traits and that these differences likely have a genetic basis. Nevertheless, the pattern of differences among populations did not fit the expectations of local adaptation. Instead, phenotypic variation seemed another outcome of genetic drift with important implications for conservation because each population should be designated as an independent evolutionary significant unit (ESU). Our study evidences the benefits of combining neutral markers with appropriate assessments of phenotype variation, and shows that even endemics with extremely narrow ranges can contain multiple conservation units. [ABSTRACT FROM AUTHOR]

Published
2015
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3. Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Author

Lopez, Lua, Barreiro, Rodolfo, Fischer, Markus, and Koch, Marcus A.

Subjects
Expressed Sequence Tags, Evolution, Population genetics, Endangered Species, Arabidopsis, Chromosome Mapping, food and beverages, Oryza, Conservation, Functional markers, 580 Plants (Botany), 570 Life sciences, Threatened plants, Gene Expression Regulation, Plant, EST-SSR, Databases, Genetic, Genetics, Data Mining, Genome, Plant, Research Article, Microsatellite Repeats, 580 Botanical sciences, Biotechnology
Abstract

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2031-1) contains supplementary material, which is available to authorized users.

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