The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes

Abstract

Dipteryx alata Vog. (Fabaceae) is a species of tree native to the Brazilian Cerrado that has economic potential due to its use for food, forage, medicinal, recovery of degraded areas, landscaping and wood extraction. The objective of the present study was to sequence, assemble and annotate the chloroplast genome sequence (cp genome) of D. alata and perform comparative analysis with the cp genome of other species of Fabaceae. The chloroplast is 158,647 bp in length and exhibits a quadripartite structure, with a pair of inverted repeats (IRs: 24,948 bp) separated by the large single copy (LSC: 88,769 bp) and small single copy (SSC: 19,982 bp) regions. It contains 125 genes, of which 109 are unique, including 76 protein-coding genes (CDS), 29 transporter RNA genes (tRNA) and four ribosomal RNA genes (rRNA). Comparative analysis of the cp genome of D. alata with the genome of other Fabaceae indicated similarity to the gene content, but gene losses and rearrangements have been identified. Comparative analysis indicated that the genes located in the IR regions were the most conserved, with average values of nucleotide diversity (Pi) of 0.03 followed by SSC (Pi-0.08) and LSC (Pi-0.09). Some non-coding regions exhibited relatively high divergence of sequences. The chloroplast genome contains also 131 simple sequence repeats (SSRs) of which 121 are located in intergenic regions and ten in protein-coding regions. The most frequent SSR repetition was A/T and AT/TA. The complete cp genome sequence of D. alata reported in this paper represents a valuable addition to the scarce available genomic resources for this Brazilian Cerrado species. This work shows the first complete plastoma of a species belonging to the ADA clade, within the Papilionoideae subfamily, and contributes to improve studies of phylogeny and plastoma evolution of the Fabaceae family. In addition, it provides new genetic information on plastid sequences useful for designing conservation and breeding strategies. Chloroplast sequences will be useful in phylogenetic studies, population genetics, phylogeography and molecular systematics.

Research Article Genome size and chromosome number of <i>Dipteryx</i> <i>alata</i> (Leguminosae): a model candidate for comparative genomics in Papilionoideae

“…Currently, studies of discovery and characterization of microsatellite markers and studies of population genetics are found in the literature for D. alata (Soares et al, 2012(Soares et al, , 2015Collevatti et al, 2013;Guimarães et al, 2017Guimarães et al, , 2019b. Genomic studies for D. alata include the assembly and characterization of the chloroplast genome (Antunes et al, 2020b). Despite advances in sequencing technology, smaller genomes have been prioritized due to lower costs for obtaining the total sequences set, which in plant includes sequences from the nuclear and organellar genomes.…”

Full-length chloroplast genome of Dongxiang wild rice reveals single-copy region switching in cpDNAs

“…In a previous study [1], 4 rRNA, 30 tRNA and 76 protein-coding genes (Table 1) have been annotated in the Onobrychis gaubae cpDNA (GenBank: LC647182) with a length of 122,688 bp and also in the O. viciifolia (GenBank: MW007721) with a length of 121,932 bp. 4 rRNA, 30 tRNA and 90 protein-coding genes have been annotated in the cpDNA of O. sativa ssp.…”

“…Chloroplast genomes (plastomes), also called chloroplast DNAs (cpDNAs) contain valuable markers for studying evolutionary relationships and population genetics of plants [1]. In contrast to mitochondrial and nuclear genomes, cpDNAs across spermatophytes (i.e.…”

“…seed plants) exhibit a higher degree of conservation with respect to their gene content, structure and organization [2]. Most cpDNAs encode about 80 protein-coding genes that are primarily involved in photosynthesis and other biochemical processes along with 30 tRNA and four rRNA genes [1]. A plant cpDNA typically has a circular structure and includes a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (denoted as IR1 and IR2) separating the LSC and SSC.…”

“…Campanulaceae [4], Onagraceae [5], Fabaceae [6] and Geraniaceae [7], only very a few of these SVs occur at the elementary-region level, for instance, an IR-lacking clade of Papilionoideae [1], which is regarded as a rarely occurring event.…”