Small Single-copy Region Research Articles

The complete chloroplast genome of Hordeum marinum ssp. marinum

Hordeum marinum ssp. marinum (Huds.) R. J. Soreng (2003) is a halophyte wild relative of barley and wheat, which exhibits remarkable salt tolerance characteristics. In this study, we presented the first characterization of the complete chloroplast genome of H. marinum ssp. marinum. Our findings reveal that the chloroplast genome of H. marinum ssp. marinum consists of a small single-copy region (SSC: 12,715 bp), a large single-copy region (LSC: 81,130 bp), and a pair of inverted repeat regions (IRs: 21,517 bp), amounting to a total length of 136,989 bp. The chloroplast genome encodes 139 genes, including 91 protein-coding genes, 38 tRNA genes, and ten rRNA genes. By utilizing phylogenetic analysis, we determine the evolutionary position of H. marinum in Triticeae. Our study provides valuable insights into the chloroplast genome of H. marinum ssp. marinum, which may have important implications for the improvement of cereal crops.

Characterization of the chloroplast genome of the marine microalga Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980

Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980, a costal green microalga, is considered as a promising animal feed in aquaculture due to the high content of fatty acids and carotenoid. Furthermore, T. marina plays important roles in bioremediation. In this study, we assembled the complete chloroplast genome of T. marina. Results showed that the full length of the complete chloroplast genome was 96,151 bp, containing a large single-copy region of 62,574 bp, a small single-copy region of 1261 bp, and a pair of inverted repeat regions of 16,158 bp. The GC content of the genome was 36.6%. A total of 125 genes were annotated, including 81 protein coding genes, 38 tRNA genes, and six rRNA genes. Phylogenetic analysis based on 22 chloroplast genomes suggested that T. marina was closely related to Tetraselmis sp. CCMP 881.

Chloroplast Genome Sequences and Phylogenetic Analysis of Eight Newly Sequenced Caryophyllaceae Species.

Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species. Using next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams, and S. lhassana (Williams) Majumdar. Bioinformatic software was used to conduct the comparative genome and phylogeny analysis of these cp genomes. The eight cp genomes were 132 188-151 919 bp in length, containing 130-132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, theinverted repeat (IR) boundaries of S. caespitella, S. atsaensis, S. lhassana, and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus. These results have provided new evidence and useful information for species identification, evolution, and genetic research on the Caryophyllaceae. In this study, eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.

New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes

Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958–84,792 bp), a small single-copy (SSC) region (18,585–18,768 bp), and a pair of inverted repeats (IRs) (25,058–25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.

Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae).

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of H. perforatum and compared the genome variation among five Hypericum species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the Hypericum chloroplast genomes. The H. perforatum chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The H. perforatum chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. Hypericum chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five Hypericum species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes-trnK-UUU, infA, and rps16-were lost, and three genes-rps7, rpl23, and rpl32-were pseudogenized in Hypericum. All the Hypericum chloroplast genomes lost the two introns in clpP, the intron in rps12, and the second intron in ycf3. Hypericum chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.

Complete chloroplast genome of Rorippa apetala Y.Y. Kim & B.U. Oh (Brassicales: Brassicaceae), a species endemic to the Korean Peninsula

Here, we successfully assembled the complete chloroplast genome of Rorippa apetala Y.Y. Kim & B.U. Oh, a species endemic to the Korean Peninsula. The chloroplast genome was 154,818 bp long and exhibited a typical quadripartite structure comprising large single-copy (83,847 bp) and small single-copy (18,023 bp) regions, and a pair of inverted repeats (26,474 bp each). A total of 129 genes were encoded, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on the concatenated sequences of 78 protein-coding genes from 25 species revealed a close relationship between R. apetala and Rorippa indica (L.) Hiern, supported by full bootstrap value (100). Future studies employing more informative markers and a broader range of taxa will provide valuable insights into the biogeographical distribution of the genus Rorippa and offer a deeper understanding of the speciation process in R. apetala.

The complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890 (Chloranthaceae)

In this study, we sequenced and assembled the complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890. The total length of the complete chloroplast sequence was found to be 158,002 bp. It consisted of a large single-copy (LSC) region of 87,127 bp, a small single-copy (SSC) region of 18,541 bp, and a pair of inverted repeat (IR) regions, each with a length of 26,167 bp. The overall GC content of the complete chloroplast genome was 38.9%, with the LSC region, SSC region, and IR regions exhibiting GC contents of 37.4%, 34.1%, and 43.1%, respectively. The annotation of the chloroplast genome revealed a total of 131 genes, comprising 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that the seven sampled species of Chloranthus were divided into two clades. Within the clade characterized by long filamentous anther connectives, C. nervosus showed the closest relation to C. japonicus. These findings validated the previous preliminary results on the phylogenetic relationships of the seven species of Chloranthus with strong support.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus chingii Hu 1925 from the family Rosaceae

Rubus chingii Hu 1925 is an important medicinal vine shrub in the Rosaceae family, widely distributed in China and Japan. In this study, the complete chloroplast genome of R. chingii was sequenced and identified. The chloroplast genome was 155,563 bp in size with a total GC content of 37.06%. Two 25,749-bp inverted repeat (IRA and IRB) regions divided the genome as four sections, with the remainder forming a large single-copy (LSC, 85,322 bp) and a small single-copy (SSC, 18,743 bp) regions. This genome contained a total of 131 genes, of which 86 were protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that R. chingii, along with several other R. longisepalus, R. tsangii, R. hirsutus, R. taiwanicola, R. rubroangustifolius, and R. glandulosopunctatus, formed the monophylic group. Interestingly, the chloroplast genome structure we reported was different from the previously reported structure and provided richer phylogenetic analysis information in the Rubus genus compared to previous studies. The genome information reported in this paper will provide some useful information for further investigation on the evolution of the family Rosaceae.

Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae)

The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.

Complete chloroplast genome and phylogenetic analysis of Meliosma oldhamii Miq. ex Maxim. (Sabiaceae)

Meliosma oldhamii Miq. is a deciduous arbor and a member of Sabiaceae. It is one of the rare and protected plants with outstanding ornamental and economic value in Jiangsu, China. In addition to the resource values indicated above, there are numerous other elements that require additional research, including the chloroplast (cp) genomic information. In this work, the complete cp genome sequence of M. oldhamii was assembled and characterized for the first time. The complete cp genome of M. oldhamii was 159,950 base pair (bp) in length, including a large single-copy (LSC) region of 87,147 bp, a small single-copy (SSC) region of 18,015 bp, and the inverted repeats (IRs) region of 27,394 bp. It contains 131 genes, including 37 tRNA genes, eight rRNA genes, 85 protein-coding genes, and one pseudogene. The overall GC content of M. oldhamii cp genome was 37.95%. The placement of M. oldhamii in the phylogenetic tree constructed using the complete cp genome is largely congruent with previous studies. The clustering of Meliosma is non-monophyletic, aligns more closely with existing morphological taxonomic studies, thereby enhancing the scholarly and scientific nature of this research.

The complete chloroplast genome of Callicarpa dichotoma (Lour.) K.Koch (Lamiaceae)

Callicarpa dichotoma (Lour.) K.Koch is a shrub species with distribution from East Asia to Southeast Asia. We assembled and annotated for the first time the complete chloroplast (cp) genome of C. dichotoma. The cp genome of C. dichotoma is 154,110 bp long with the GC content of 38.09% and consists of four subregions: a large single-copy (LSC) region of 84,915 bp, a small single-copy (SSC) region of 17,783 bp and a pair of inverted repeats (IRs) of 25,706 bp each. The cp genome of C. dichotoma encodes a total of 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic trees based on the coding sequences strongly support the position of C. dichotoma within the genus Callicarpa, confirming the previously reported monophyly of the genus.

Sarcolobus globosus subsp. peregrinus, a newly recorded subspecies of Sarcolobus (Apocynaceae) from Zhanjiang, China

A newly recorded subspecies, Sarcolobus globosus subsp. peregrinus (Blanco) Rintz, was reported. This subspecies was previously known to be distributed in Southeast Asia islands, which was recently found in Zhanjiang, Guangdong, China. Detailed morphological description, field photos and geographical distribution are provided in this study. Additionally, the whole chloroplast genome was sequenced by the Illumina sequencing technology. The annotated results revealed that the chloroplast genome has a conserved quadripartite structure, with a pair of inverted repeat regions (IRs) separating the large single copy (LSC) region from the small single-copy (SSC) region, resulting in a total length of 161,561 base pairs (bp). The phylogenetic analysis shows that S. globosus subsp. peregrinus is clustered with its type subspecies (i.e., subsp. globosus), and the significant difference in branch length between them indicates a large variation in their evolutionary rates. These results provide new insights into the Apocynaceae of China.

Comparative analysis of chloroplast genomes of two Chinese local citrus varieties and haplotype analysis with other citrus species

Citrus plants, comprising some of the most widely cultivated fruit crops worldwide, have great research value. We assembled and annotated the chloroplast genomes of two local important citrus varieties of China, ‘Tuju’ and ‘Zangju’, and comparatively analyzed their sequences. The full lengths chloroplast genomes of ‘Tuju’ and ‘Zangju’ were 160,121 and 160,694 bp, respectively. Both featured a quadripartite structure with two copies of a large inverted repeat (IR) separated by small (SSC) and large (LSC) single-copy regions. ‘Tuju’ chloroplast genome contained 134 genes. ‘Zangju’ had one less protein-coding gene (rpl22) than ‘Tuju’. We also found 27 and 21 optimal codons, all of which ended with A or U, for chloroplast protein-coding genes of ‘Tuju’ and ‘Zangju’, respectively. There were 32 haplotypes obtained from 43 citrus chloroplast genomes, some different species or cultivars could share one haplotype. Of them, ‘Tuju’, one individual of Citrus limon, one individual of Citrus maxima and Citrus platymamma shared one haplotype, which implied they had the same maternal origin. The phylogenetic trees supported that all haplotypes could be divided five groups, while haplotype network analysis tended to get three groups. Our study reveals the complex lineage relationship of citrus plants at a certain level, and provides a valuable reference tool for future research on citrus plants.

The complete chloroplast genome of Scutellaria barbata D. Don 1825 revealed the phylogenetic relationships of the Scutellaria genus

Scutellaria barbata D. Don 1825 is an important medicinal plant distributed in wetlands about 2000 m above sea level and used to treat various diseases. The complete chloroplast genome of S. barbata is 152,050 bp with four subregions consisting of a large single-copy region (84,053 bp), a small single-copy region (17,517 bp), and a pair of inverted repeats (25,240 bp). In the chloroplast genome of S. barbata, 131 genes were detected, comprising 87 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 36 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome and protein-coding DNA sequences of 27 related taxa of the genus (out group included Holmskioldia sanguinea and Tinnea aethiopica) indicates that S. barbata was made a clade with S. orthocalyx, and S. meehanioides was a sister to them. The first chloroplast genome of S. barbata was reported in this work, serving as a potential reference for important medicinal plants within the Scutellaria genus.

The complete chloroplast genome of Allium wallichii Kunth (Amaryllidaceae)

Allium wallichii Kunth is a herb species with potentially extensive applications because of its edible, ornamental, and pharmaceutical values. The structural characteristics and phylogenetic relationships of its chloroplast genome were determined here for the first time. The complete cp genome was found to be 152,496 bp long, with a GC content of 37.04%. It consists of four distinct regions: a large single copy (LSC) region of 82,510 bp, a small single copy (SSC) region of 17,460 bp, and two inverted repeat (IR) regions of 26,263 bp each. The genome encodes 129 genes, including 86 protein-coding genes, 37 tRNA genes, and six rRNA genes. Our phylogenetic analysis revealed that A. wallichii was closely related to Allium wallichii var. platyphyllum, which are included in the section Bromatorrhiza, subgenus Amerallium Traub of the genus Allium. Our report provides valuable information on the genetic diversity of Allium species.

The complete chloroplast genome of Ocimum americanum Linnaeus 1755 and phylogenetic analysis among the Lamiaceae family

Ocimum americanum Linnaeus 1755 (Lemon basil) is an essential medicinal species in the Ocimum genus. Its leaf decoction is traditionally used to treat diabetes, constipation, diarrhea, piles, and dysentery. The essential oils from this species have intense fungicidal activity. The complete chloroplast genome sequence of O. americanum was assembled from Illumina paired-end sequencing data. The O. americanum chloroplast genome was 152,460 bp in length, containing a large single copy (LSC) region of 83,459 bp and a small single copy (SSC) region of 17,607 bp, separated by a pair of inverted repeats (IRs) of 25,697 bp. The genome contained 134 unique genes, including 89 protein-coding, 37 tRNA, and eight rRNA genes. Among them, nine genes had a single intron, and two genes contained two introns. The overall GC content of the chloroplast genome was 38%, while the corresponding values of LSC, SSC, and IR regions were 35.8%, 31.7%, and 43.1%, respectively. In the phylogenetic analysis, all the Ocimum species formed a group closely related to Plectranthus barbatus. O. americanum was more closely related to O. gratissimum and O. basilicum than the other species of Ocimum included in this study.

Comparative analysis of switchgrass chloroplast genomes provides insights into identification, phylogenetic relationships and evolution of different ecotypes

Switchgrass (Panicum virgatum L.) plays a crucial role as a valuable forage and bioenergy resource. There are two ecotypes of switchgrass, upland and lowland, which exhibit significant differences in their adaptability to various environmental stressors. To enhance ecotype identification and gain a comprehensive understanding of the evolutionary relationships between these two ecotypes at the population level, we assembled 20 switchgrass chloroplast genomes (10 uplands and 10 lowlands) collected from different latitudinal regions. All chloroplast genomes displayed the typical quadripartite structure, with sizes ranging from 139,497 bp (J170. A) to 139,746 bp (J440. A and J636. B). The annotation of these 20 switchgrass chloroplast genomes revealed a consistent number of genes, including 40 transfer RNAs, eight ribosomal RNAs, and 86 protein-coding genes. Through multiscale analyses of the chloroplast genomes, we observed conservation in the upland and lowland chloroplasts in terms of IR boundaries, repetitive sequences, and codon usage. Our comparative chloroplast genome analysis revealed that large single copy regions exhibited the highest nucleotide diversity, followed by small single copy regions, while inverted repeat regions showed a relatively conserved pattern. Additionally, we identified a hotspot, trnG-GCC-trnM-CAU, which was exclusive to the lowland ecotype, suggesting its potential to differentiate between the two ecotypes. In the phylogenetic analysis, we found that some accessions from both ecotypes were intermixed and clustered into one clade, highlighting the complexity of the phylogenetic evolution process. In conclusion, we employed population-level comparative genomic analysis to investigate genetic variations and phylogenetic relationships among different ecotypes, thereby offering novel insights into the evolutionary dynamics and classifications of switchgrass.

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.

The complete chloroplast genome sequence of <i>Rhododendron caucasicum</i> (Ericaceae)

<i>Rhododendron caucasicum</i> Pall. is a shrub distributed in the mountainous areas of the Caucasus from northeastern Türkiye towards the Caspian Sea. This study reports the first complete chloroplast genome sequence of <i>R. caucasicum</i>. The plastome is 199,487 base pairs (bp) long and exhibits a typical quadripartite structure comprising a large single-copy region of 107,645 bp, a small single-copy region of 2,598 bp, and a pair of identical inverted repeat regions of 44,622 bp each. It contains 143 genes, comprising 93 protein-coding genes, 42 tRNA genes, and eight rRNA genes. The large chloroplast genome size is likely due to the expansion of inverted repeats. A phylogenetic analysis of chloroplast genomes with other <i>Rhododendron</i> species supports previously recognized infrageneric relationship.

Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae.

Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.