The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree

Abstract

The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree Prosopis cineraria is native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the P. cineraria genome to near-chromosomal assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-)-retrotransposons. We find an expansion of terpenoid metabolism genes in P. cineraria and its relative Prosopis alba, but not in other legumes. We also observed an amplification of NBS-LRR disease-resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya. These retrogenes include many biotic defense responses and abiotic stress stimulus responses, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to the low nitrogen in arid desert soil. Consistent with these results, our differentially expressed genes show a tissue specific expression of isoprenoid pathways in shoots, but not in roots, as well as important genes involved in abiotic salt stress in both tissues. Overall, the genome sequence of P. cineraria enriches our understanding of the genomic mechanisms of its disease resistance and abiotic stress tolerance. Thus, it is a very important step in crop and legume improvement.

Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera

“…However, according to the phylogenomic analysis performed by Catalano et al 13 , there are more distant relationships among species from the Old World sections and closer relationships among species of the American sections (Strombocarpa, Algarobia, and Monilicarpa sections). Prosopis cineraria is one of the most common trees of the Indian desert, Arabian Peninsula and, in general, is abundant throughout the middle east 60,77 , whereas N. juliflora is native to the Caribbean, Central and northern South America 78 . However, Neltuma juliflora was introduced to Ethiopia and the Middle East around 1970 and over the years this species has spread outside the plantation areas, adversely affecting natural habitats and rangelands 79 .…”

Comparative analysis of the complete plastid genomes of desert trees Neltuma and Strombocarpa genera

“…However, according to the phylogenetic analysis performed by Catalano et al 13 , there are more distant relationships among species from the Old World sections and closer relationships among species of the American sections (Strombocarpa, Algarobia, and Monilicarpa sections). Prosopis cineraria is one of the most common trees of the Indian desert, Arabian Peninsula and, in general, is abundant throughout the middle east 57,71 , whereas N. juli ora is native to the Caribbean, Central and northern South America 72 . However, Neltuma juli ora was introduced to Ethiopia and the Middle East around 1970 and over the years this species has spread outside the plantation areas, adversely affecting natural habitats and rangelands 73 .…”

“…Later, P. farcta diverged in the Early Oligocene (mean = 33.52 Mya; 95% HPD = 29.48-37.70 Mya), while P. cineraria diverged together with the Neltuma species in the Pleistocene. Sudalaimuthuasari et al71 , using whole genome sequencing with 76,554 genes, estimated that P. cineraria and P. alba diverged ~ 23Mya. Undoubtedly, this divergence time is closer to what would be expected for species of the genus Prosopis that belongs to the Old World, but not for P. cineraria, whose complete chloroplast genome data show a divergence time of 1.85 Mya (95% HPD: 1.56-2.12 Mya), strengthening our suspicion of this sample being a natural hybrid.…”

Physiology, genomics, and evolutionary aspects of desert plants

“…The genome sequence of a few desert-adapted plants has already been reported ( Table 1 ). They are Welwitschia mirabilis [148] , Linathus parryae [149] , Prosopis cinera [150] , and others ( Table 1 ). Welwitschia mirabilis is a desert plant with extreme longevity with two ever-elongating leaves.…”