Abstract
BackgroundProsopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus.ResultsNext generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads.Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic.ConclusionsThis study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data.The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics resources for P. alba functional analysis and genetics. Finally, it will also potentially contribute to the development of population-based genome studies in the genera.
Highlights
Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species
These isogroups are equivalent to genomic loci with an average of 1.2 transcripts per locus, which potentially reflect multiple splicing variants
Within the sequences associated with biological processes, we found Gene Ontology (GO) terms associated with primary and secondary metabolism
Summary
Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. The genus Prosopis Linnaeus emend Burkart, a member of the subfamily Mimosoideae within the family Fabaceae, comprises 44 species divided into 5 sections: Prosopis, Anonychium, Strombocarpa, Monilicarpa and Algarobia [1] This genus is spread around the world in arid and semiarid regions, including North and South America, North and Central Africa, Near East and the Caribbean region. The main center of diversity for Prosopis genus is located in Argentina [1] with 27 species Of these species, 21 belonging to Algarobia section [2], which are distributed in the phytogeographic provinces of Chaco, Monte, and Espinal [3]. One of the most important features of this genus is its natural capacity to produce fertile interspecific hybrids [5,6,7] This generates a syngameon complex integrated by species and subspecies which form a continuum [8]. This complex includes six taxonomic species that play a significant role in Argentina: P. alba, P. hassleri, P. nigra, P. ruscifolia, P. chilensis and P. flexuosa
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