Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

Introduction

Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety.

Methods

The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum.

Results and discussion

The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium.

Conclusion

Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.

Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae)

BACKGROUND

The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed.

RESULTS

Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness.

CONCLUSIONS

Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Introduction

The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae.

Methods

In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses.

Results

The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic.

Discussion

Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

Complete chloroplast genome of Lonicera ligustrina Wall. (Caprifoliaceae) and its phylogenetic implications

Lonicera ligustrina is a folk medicinal herb in China and India with highly potential medicinal value. Here, we reported the complete chloroplast (cp) genome of L. ligustrina (GenBank accession number: ON968694). The cp genome was 155,330 bp long, with a large single-copy region (LSC) of 88,855 bp and a small single-copy region (SSC) of 18,647 bp separated by a pair of inverted repeats (IRs) of 23,914 bp. We also reconstructed the phylogeny of Lonicera using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The current study indicated that L. ligustrina is sister with the Nintooa clade of subgen. Lonicera.

A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion

PREMISE

The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion.

METHODS

We inferred the phylogeny of Lonicera using restriction site-associated DNA sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits.

RESULTS

RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (Periclymenum and Chamaecerasus), three of the four sections (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa, a clade of ~22 mostly vine-forming species, including L. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules.

CONCLUSIONS

We provide the most comprehensive and well-supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in depth developmental and functional analyses.

Complete chloroplast genome and phylogenetic analysis of Lonicera caerulea var. edulis (Caprifoliaceae)

Lonicera caerulea var. edulis, known as "blue honeysuckle" or "Haskap," is a deciduous shrub that belongs to the Caprifoliaceae family. Characterized by the high cold hardiness and high quality of fruit, it has become a novel cash crop in cold regions worldwide. The lack of available chloroplast (cp) genome information limits studies of its molecular breeding and phylogeny. Here, the complete cp genome of Lonicera caerulea var. edulis was assembled and characterized for the first time. It was 155,142 bp in length with 38.43% of GC content, including 23,841 bp inverted repeat regions (IRs), an 88,737 bp large single-copy region (LSC), and an 18,723 bp small single-copy region (SSC). A total of 132 genes, including 85 protein-coding genes, 8 rRNA genes, and 39 tRNA genes were annotated. Phylogenetic analysis indicated that L. caerulea var. edulis was closely related to L. tangutica. These data and results provide a valuable resource for the development of breeding tools and genetic diversity studies for L. caerulea.

Comparative chloroplast genomes and phylogenetic analyses of Pinellia

Background

Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.

Methods and results

We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.

Conclusions

The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.

Supplementary Information

The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.

Complete Chloroplast Genome Sequence of Triosteum sinuatum, Insights into Comparative Chloroplast Genomics, Divergence Time Estimation and Phylogenetic Relationships among Dipsacales

Triosteum himalayanum, Triosteum pinnatifidum (Triosteum L., Caprifoliaceae, Dipsacales) are widely distributed in China while Triosteum sinuatum mainly occurrs in northeast China. Few reports have been determined on the genus Triosteum. In the present research, we sequenced 2 chloroplast genomes of Triosteum and analyzed 18 chloroplast genomes, trying to explore the sequence variations and phylogeny of genus Triosteum in the order Dipsacales. The chloroplast genomes of the genus Triosteum ranged from 154,579 bp to 157,178 bp, consisting of 132 genes (86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes). Comparative analyses and phylogenetic analysis supported the division of Dipsacales into two clades, Adoxaceae and six other families. Among the six families, a clade of Valerianaceae+Dipsacaceae was recovered as a sister to a clade of Morinaceae+Linnaeaceae. A closer relationship of T. himalayanum and T. pinnatifidum among three species was revealed. Our research supported that Loniceraferdinandi and Triosteum was closely related. Zabelia had a closer relationship with Linnaea borealis and Dipelta than Morinaceae. The divergence between T. sinuatum and two other species in Triosteum was dated to 13.4 mya.

Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species

BACKGROUND

The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species.

RESULTS

The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus.

CONCLUSION

The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

On the Edge of Dispensability, the Chloroplast ndh Genes

The polypeptides encoded by the chloroplast ndh genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack ndh genes. Among vascular plants, the ndh genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid ndh genes allows comparison on phylogenetic trees and functional investigations of the ndh genes. The ndh genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, ndh genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without ndh genes at risk of extinction and, probably, most extant ones may have lost ndh genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking ndh genes challenge models about the role of ndh genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of ndh genes.

Analysis of the complete chloroplast genomes of Scutellaria tsinyunensis and Scutellaria tuberifera (Lamiaceae)

Scutellaria Linn. is a perennial herb with about 300 species. This genus has high medicinal value and many are used in Traditional Chinese Medicine (TCM). In this study, we sequenced and assembled the complete chloroplast genomes of Scutellaria tsinyunensis and S. tuberifera. Subsequently, we conducted a comprehensive comparative genomics analysis with 12 other published Scutellaria species. These genomes all had a conserved quartile structure, and the gene contents, gene sequences and GC contents are highly similar. The study on the genetic characteristics and nucleotide substitution rate of different genes found that the protein-coding genes of chloroplasts have differed greatly. Most genes are under purifying selection, but the rps12 gene may have undergone positive selection. Besides, we identified three hypervariable regions as potential markers for Scutellaria taxa, which could play an important role in species identification of Scutellaria. Phylogenetic analysis showed that the 14 Scutellaria taxa were divided into two major clades. Moreover, the variation of IR regions is closely related to the evolutionary history as was reconstructed based on SNPs. In conclusion, we provided two high-quality chloroplast reference genomes of Scutellaria, this reliable information and genomic resources are valuable for developing of efficient DNA barcodes as reconstruction of chloroplast evolutionary history of the genus.

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae: Anthurium huixtlense (size: 163,116 bp) and Pothos scandens (size: 164,719 bp). The chloroplast genome of P. scandens showed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats in P. scandens when compared with A. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 in P. scandens and 2.12 in A. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.

Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses

Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), along with a total of 51-61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of Dolomiaea as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, rpoC2 and ycf1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.

Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.