Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (Subfamily: Caesalpinioideae)

Abstract

Background Neltuma pallida is a tree that grows in arid soils in northwestern Peru. Being a predominant species of the Equatorial Dry Forest ecoregion, it has a high economic and ecological importance for people and environment. Despite this, the species is severely threatened and there are few genetic and genomic studies about it, making it difficult to propose evidence-based conservation strategies.Results In this work, the chloroplast genome of a N. pallida specimen was assembled, annotated, analyzed and compared with those of related species. The length of the assembled chloroplast genome was 162381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC% for the genome was 35.97%, although this is variable between regions, with a higher GC% found in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 18 contained at least one intron in their sequence. A large number of repetitive sequences of different types were identified in the assembled genome, being the most frequent the tandem repeats (> 300), especially microsatellites (SSR). The phylogenetic reconstruction of Prosopis s.l. showed that this group is monophyletic. N. pallida was closely related to P. cineraria, N. juliflora and N. glandulosa, forming a subclade with these species. When comparing the chloroplast genome sequence of N. pallida with N. juliflora, P. farcta and Strombocarpa tamarugo, it was found that the sequences were highly similar.Conclusions The chloroplast genome of N. pallida is composed of 162381 bp with the classical quadripartite structure and GC% of 35.97%, a value similar to that of other closely related species. Also, the genetic structure of the genome was found to be similar to other members of Prosopis s.l. In the chloroplast genome of N. pallida, more than 800 repetitive sequences were identified, being the most common the tandem repeats. N. pallida showed closeness to the other Neltuma spp., forming a subclade within the Prosopis s.l. group. The divergence analysis indicated that there were little differences when comparing the Prosopis s.l. chloroplast genomes, evidencing high levels of conservation between these species.