The First Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Pistachio (Pistacia vera)

Abstract

Pistachio is one of the most economically important nut crops worldwide. However, there are no reports describing the chloroplast genome of this important fruit tree. In this investigation, we assembled and characterized the complete pistachio chloroplast sequence. The Pistacia vera chloroplast genome was 160,598 bp in size, similar to other members of Anacardiaceae (149,011–172,199 bp) and exhibited the typical four section structure, including a large single copy region (88,174 bp), a small single copy region (19,330 bp), and a pair of inverted repeats regions (26,547 bp). The genome contains 121 genes comprised of 87 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Thirteen intron-containing genes were identified in the genome wherein two genes had more than two introns. The genomic patterns of GC content resembled those for other Anacardiaceae. P. vera displayed the highest number of simple sequence repeats (SSRs) among the genera studied, which may be useful for molecular marker development and future population studies. Amino acid analysis revealed that Leucine is the most frequent (10.69%) amino acid in the chloroplast genome followed by Isoleucine (8.53%) and Serine (7.77%). Cysteine (1.30%) and Tryptophan (1.74%) were the least frequent amino acids. Phylogenetic analysis revealed P. vera is most like its taxonomically close relative P. weinmaniifolia, followed by Rhus chinensis; all placed taxonomically in the tribe Rhoeae. Members of Anacardiaceae were most closely related to Rhoeae, followed by members of Spondieae. The reports of this chloroplast genome will be useful for future conservation studies, genetic evaluation and breeding of P. vera, and more comprehensive phylogenetic analysis of the Pistacia species and its closely-related genera.

Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan

“…SSRs and oligonucleotide repeats may be useful in phylogenetics and functional genomics [ 21 , 57 , 64 ]. SSRs were engaged in a variety of cp genome alterations, deletions, insertions, and substantial variants [ 65 , 66 ].…”

“…SSRs were engaged in a variety of cp genome alterations, deletions, insertions, and substantial variants [ 65 , 66 ]. The most prevalent SSR type was mononucleotides, which had two repeat patterns, A and T. Several higher plants showed comparable outcomes, revealing the prevalence of adenine and thymine repeats in cp genomes [ 21 , 57 , 61 , 64 – 66 ]. Hexanucleotide SSRs, which are lacking in some other cp genomes [ 57 , 61 , 65 , 67 ] were not found in the S. sesuvioides genome.…”

“…The most prevalent SSR type was mononucleotides, which had two repeat patterns, A and T. Several higher plants showed comparable outcomes, revealing the prevalence of adenine and thymine repeats in cp genomes [ 21 , 57 , 61 , 64 – 66 ]. Hexanucleotide SSRs, which are lacking in some other cp genomes [ 57 , 61 , 65 , 67 ] were not found in the S. sesuvioides genome. Sequence repeats were more abundant in single-copy sections than in inverted repeats, supporting the notion that IRs are preserved.…”

“…The cp genome sequences are an important source of data for phylogenetic studies [ 21 , 55 , 57 , 76 ]. The emergence of scale-up sequencing methods has increased access to cp genomes with massive amounts of genetic influence [ 55 , 63 , 77 ].…”

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

“…These cp SSRs (simple sequence repeats) are informative molecular markers for evaluating genetic relationships due to their high polymorphism and copy number variation. The identified cp SSR loci could prove highly valuable for genetic diversity studies and may enhance the effectiveness of interspecific discrimination, potentially in combination with other nuclear genomic SSRs (Zarei et al, 2022).…”