OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes

The Complete Chloroplast Genome of Idesia polycarpa and Comparative Analysis of Related Species

BACKGROUND/OBJECTIVES

The oil grape (Idesia polycarpa), often called the "golden tree", is an essential woody plant valued for its edible oil. Although its economic significance is recognized, the specifics of its chloroplast genome and evolutionary connections remain unclear. This study sequenced the chloroplast genome of I. polycarpa and performed a comparative analysis of its genome structure, genetic diversity, and phylogenetics using chloroplast data from related species.

METHODS

In this study, we sequenced and annotated the whole chloroplast genome of I. polycarpa via GISEQ-500 sequencing and de novo assembly.

RESULTS

The chloroplast genome of I. polycarpa exhibits a typical tetrad structure, with a length of 155,899 bp and a GC content of 36.78%. It comprises 130 unique genes, including 85 coding genes, 37 tRNAs, and eight rRNAs, showing notable conservation in gene composition and arrangement compared to closely related species. However, the inverted repeat region boundaries are narrower. Phylogenetic analysis showed strong relationships among I. polycarpa, Bennettiodendron brevipes, Poliothyrsis sinensis, Itoa orientalis, and Carrierea calycina within the Salicaceae family. Additionally, positive selection analysis revealed that rpl16, ycf1, rps18, and rpl22 are under significant selective pressure in related species, likely linked to adaptations for photosynthesis and environmental responses.

CONCLUSIONS

This research provides vital molecular foundations for the conservation, classification, and enhancement of I. polycarpa germplasm resources, advancing the study of adaptive evolutionary mechanisms and broadening the genomic database for I. polycarpa.

Population structure and mitogenomic analyses reveal dispersal routes of Macrobrachium nipponense in China

BACKGROUND

The oriental river prawn Macrobrachium nipponense is widely distributed in China, but its origin and distribution routes remain largely unknown. We collected 126 oriental river prawn specimens from four lakes and one river across China, and sequenced their mitochondrial cytochrome C oxidase subunit I (cox1) genes. We performed whole-genome resequencing of 100 samples and assembled mitogenomes for population analysis, these two types of mitochondrial markers (cox1 and all 13 protein-coding genes-13 PCGs), a nuclear marker (28S rRNA) and SNPs to infer the relationships between the five populations, the population structure, and migratory routes. We also assembled complete mitogenome per sampled population (5 in total) and used them to conduct comparative mitogenomic analyses.

RESULTS

The complete mitogenomes comprised 15,774-15,784 base pairs (bp). The average nucleotide diversity (π) of the populations, inferred using the cox1 gene data, was 0.03013 ± 0.00618, ranging from 0.00500 ± 0.00110 (Fuxian Lake) to 0.03562 ± 0.02538 (Khanka Lake). The identified haplotypes (33 cox1 and 101 13 PCGs) clustered into three main geographical lineages. Lineage A included Khanka Lake and one clade from the Haihe River. The specimens from Fuxian Lake constituted lineage B. Lineage C comprised a majority of specimens from the Haihe River, Taihu Lake, and Poyang Lake, and a minority of specimens from Khanka Lake and Fuxian Lake.

CONCLUSIONS

This study indicates that native M. nipponense prawns in China originated from East China, subsequently spreading northward and westward into the inland regions along the Grand Canal and the Yangtze River system, forming distinct lineages. This proposed route improves our understanding of the geographic distribution and origin of M. nipponense in China.

Comparative and phylogenetic analysis of complete chloroplast genomes of Phrynium s. s. and Stachyphrynium (Marantaceae) in China, including a new species

Plants of the genera Phrynium and Stachyphrynium traditionally used as ethnomedicine or for wrapping sticky rice dumpling in the tropical and south subtropical Asia, have a long history of ethnobotanical use. China represents the northernmost distribution of Marantaceae in Asia. Due to the notably similar leaf morphology between these genera, herbarium specimens are frequently misidentified, especially during the vegetative stages. Their morphological uniformity and unclear interspecific genetic relationships pose significant challenges to taxonomic classification and species identification. To date, systematic taxonomic revisions and phylogeny of their indigenous species remain lacking. In this study, we conducted comparative chloroplast genomes analyses of seven Phrynium and two Stachyphrynium species in China. The chloroplast genomes exhibited conserved structure, gene content, gene order and codon usage bias, but diverged in genomes size and the SC/IR boundaries. Four variable regions were identified as potential molecular markers for species identification. Phylogenetic analyses using CDS and nrDNA strongly support Phrynium and Stachyphrynium in China as two distinct monophyletic groups, with Phrynium subdivided into two clades. These findings advance our understanding of their molecular relationships and provide critical insights for identification, utilization, and conservation as medicinal plants. Finally, we describe and illustrate the new species Phrynium pyramidale Y. Tong & Z. Y. Lin.

Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses

Several quadriflagellate genera were revealed as the members of deep branches in Chlamydomonadales. However, the phylogenetic relationships among these quadriflagellate genera remained unresolved, and little information is known about the chloroplast genome structure for the chlamydomonadalean early-diverging lineages due to the limited data. In this study, we conducted phylogenetic and comparative genomic analyses with 6 newly sequenced quadriflagellate chlamydomonadalean chloroplast genomes. Four phylogenetic inferences based on different datasets recovered the robust topology, with Staurocarteria-Hafniomonas as the earliest-diverging lineage, followed by Corbierea within Chlamydomonadales and Spermatozopsis included in Sphaeropleales. The amino acid dataset combined with the site-heterogeneous model received the highest support for key nodes and may better fit the inferences of the deep relationships in Chlamydomonadales. Moreover, Sp. similis chloroplast genome is also more structurally similar to its close relatives than to other quadriflagellate chlamydomonadaleans. Phylogeny and genome structure features both indicated the taxonomic position of Spermatozopsis should be reconsidered. The loss of large inverted repeats (IRs) was first reported in chlamydomonadaleans (Co. pseudopalmata), and may occur at least 4 times in Chlamydomonadales. Comparative genome analyses demonstrated the highly divergent large IRs and a high level of rearrangements across the entire genome. IR expansions/contractions and inversions contribute to changes in gene content and gene order in this region. This study provides a foundation for future research on the phylogenetic relationships as well as chloroplast genomic features and evolution of the entire Chlamydomonadales.

Comparative analysis of complete chloroplast genomes of Cousinia (Asteraceae) species

The study focused on analyzing the chloroplast genome structure and investigating the phylogenetic relationships among six species of the Cousinia genus. Within the Asteraceae family, the complete chloroplast genome sequences of six Cousinia species, ranging from 152,553 to 152,619 bp. The chloroplast genomes exhibit a characteristic quadripartite structure. The gene order is largely conserved across the genus, with an exception in the small single copy region, where a reverse orientation is observed in comparison to Cousinia thomsonii. A total of 131 genes were annotated, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, with 18 genes showing duplication. Notably, 16 genes contain introns, with ycf3 and clpP carrying two introns each. Nucleotide diversity analysis revealed 412 polymorphic sites across 152,892 nucleotides in six Cousinia species. Higher nucleotide polymorphism levels were found in trnE-UUC - rpoB, trnL-UAA - trnF-GAA - ndhJ, rbcL, and ycf1 genomic regions, indicating possible genomic loci for species differentiation. Phylogenetic analysis using complete chloroplast genomes, demonstrated the genus Cousinia's phylogenetic placement within the Cardueae tribe, forming distinct clades that align with its traditional sectional classification. The Arctiinae subtribe, containing Cousinia, forms a monophyletic group with Arctium lappa, while Saussureinae were found to be polyphyletic. The findings suggest that while morphological traits are valuable in taxonomy, they may provide limited resolution compared to the more comprehensive phylogenetic insights obtained from chloroplast genome analysis.

Comparative analysis of chloroplast genomes in three Araceae species: genomic difference, genetic distance and species morphology association

Many species in the Araceae have extremely high medicinal value, while the chloroplast genome is relatively conserved, and the encoded and expressed bioactive substances are also abundant. Therefore, chloroplast genomes can serve as one of the basis for species evolution and are extremely important for individual material accumulation. To study the relationship between the chloroplast genome and morphology of target species, this study selected three Araceae species for chloroplast genome sequencing assembly, downloaded the complete chloroplast genomes sequences of another 11 Araceae species. Grouping based on genetic distance, we analyze the association between chloroplast genome structure and morphology. The results showed that there were significant differences in genome size among the three species, but Relative Synonymous Codon Usage (RSCU) exhibited high similarity; Based on the phylogenetic tree, these 14 species can be divided into three branches, with differences in genes such as rrn4, rrn5, rrn23, and trnN among species within each branch; Morphologically, the length of the male inflorescence in BranchⅢ is significantly greater than that in BranchⅡ; There is a strong positive correlation between the length of the plant stem and the three parameters (Length of LSC, Length of SSC and Length of chloroplast genome) of the genome. This study conducted correlation research from the perspective of chloroplast genome and species morphology. On the one hand, the genetic distance and chloroplast genome structure differences between the target species were determined, and on the other hand, explored the correlation between chloroplast genome and species morphology, providing a theoretical basis for the study of phylogenetic relationships and morphology of Araceae species.

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species in China, with 13 being endemic. The high diversity of this genus presents taxonomic challenges, particularly in the M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze the chloroplast genomes of Melanoseris, with a focus on the M. cyanea group, to explore structural differences and phylogenetic relationships among these closely related species. We analyzed the chloroplast genomes of 16 Melanoseris samples, including 12 new genomes from the M. cyanea group. The genome sizes ranged from 152,255 to 152,558 bp and exhibited a typical quadripartite structure, with an average GC content of 37.7%. Each genome encodes 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analysis identified 89 to 105 dispersed repeats, 24 to 28 tandem repeats, and 35 to 39 SSRs, with mononucleotide A/T repeats being the most common. Sequence alignment revealed that variable regions were mainly concentrated in the single-copy regions. Nucleotide diversity ranged from 0 to 0.00485, highlighting 10 mutation hotspot regions. Phylogenetic analysis showed a limited differentiation among species within the M. cyanea group. This research enhances our understanding of the genetic diversity of Melanoseris, laying the foundation for future taxonomic and phylogenetic studies.

Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort

Lettuce (Lactuca sativa var. ramosa Hort) is an important leaf vegetable that widely cultivates due to its high-quality, short growth cycle, and less diseases. L. sativa var. ramosa Hort belongs to Asteraceae family and its evolutionary relationships with related species of Asteraceae are not completely assessed based on genome sequences. Here, we assembled the whole mitochondrial (mt) genome of L. sativa var. ramosa Hort, and performed a comparative with other related species. The L. sativa var. ramosa Hort mt genome has a typical circular structure with a length of 363,324 bp, within GC content accounted for 45.35%. In total of 71 genes, comprising 35 protein-coding genes (PCGs), 6 rRNAs, 28 tRNAs, and 2 pseudogenes were annotated. Codon preference, RNA-editing sites, repetitive sequences, and genes migrating from chloroplast (cp) to mt genomes were investigated in the L. sativa var. ramosa Hort mt genome. Nucleotide diversity (Pi) showed that the L. sativa var. ramosa Hort mt genome was relatively conserved. A Bayesian phylogenetic tree showed that L. sativa var. ramosa Hort was closely to L. sativa var. capitata and L. virosa, which belonged to the Lactuca genus in the Asteraceae family. Our findings will provide useful information to explore genetic variation, genetic diversity, and molecular breeding on the Lactuca genus.

Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema

Arisaema takesimense (Araceae) is a unique species found exclusively in Ulleung Island of Korea. This study presents the complete chloroplast (cp.) genome of A. takesimense, which comprises 174, 361 base pairs and exhibits a typical tetrad structure. The genome encodes 112 unique genes, including 78 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. In this study, a total of 49 long repeats and 139 simple sequence repeats (SSRs) were identified, predominantly located in intergenic spacer regions (IGS). Additionally, several hotspot regions, including trnS-G, accD-psaI, ndhF and rps15-ycf1, were identified, which are commonly shared among Araceae species. The analysis of these repeats revealed species-specific SSR types and hotspot regions that can be utilized for population genetic studies and species identification. A comparative genomic analysis of eleven Arisaema taxa revealed that the large single copy region (LSC) exhibits the most variability, with non-coding genes displaying more variation than coding genes. The borders between the LSC-IR-SSC regions in Arisaema taxa were generally well-preserved, and there were notable exceptions in the positions of LSC/IRa, LSC/IRb and SSC/IRb junctions for A. takesimense, A. ringens, and A. nepenthoides. A phylogenetic analysis based on the cp. genome revealed a close relationship between A. takesimense and A. bockii. The outcomes of this study substantially increase the genomic resources available for Araceae, serving as a valuable resource for species identification and evaluating intraspecific diversity within the Arisaema genus.

Decoding the Chloroplast Genome of Korean endemic plant Acer okamotoanum: Comparative Genomics, Phylogenetic Insights, and Potential for Marker Development

Acer okamotoanum, a medicinally significant endemic plant of Korea, has seen limited genomic research. To address this gap, we conducted a comprehensive sequencing and analysis of its chloroplast genome. The assembled genome is 156,242 bp in length, with typical quadripartite structure, consisting of a large single-copy region, a small single-copy region, and two inverted repeat regions. It contains 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Sixteen genes have a single intron, while clpP and ycf3 possess two introns each. Additionally, 17 genes are duplicated within the inverted repeat regions. The genome analysis revealed 92 Simple Sequence Repeats (SSRs), predominantly located in intergenic regions, with a bias toward A/T-rich codons. Comparative analysis with five closely related Acer species highlighted a highly conserved genomic structure, but also revealed differences in SSRs and repeat sequences. Hypervariable regions, such as rpl32-trnL and ycf1, were identified as potential molecular markers for phylogenetic and population studies. Phylogenetic analysis involving 37 chloroplast genomes confirmed the monophyly of the Acer genus and placed A. okamotoanum within the Platanoidea section, closely related to A. truncatum. This study improves the understanding of A. okamotoanum's genomic structure, offering insights for phylogenetic analysis, marker development, and conservation efforts.

Characterization of the complete chloroplast genome of Chasmanthium latifolium (Michx.) H.O.Yates, 1966 (Poaceae)

Chasmanthium latifolium (Michx.) H.O.Yates is a popular ornamental plant native to southeastern North America. Genomic data and genetic studies related to Chasmanthium latifolium are limited. Therefore, the complete chloroplast genome of Chasmanthium latifolium was sequenced, assembled, and characterized in this study. The complete chloroplast genome was 138,934 bp in length and contained 105 unique genes (77 protein-coding genes, 24 tRNA genes, and 4 rRNA genes). Phylogenetic analyses showed that Chasmanthium latifolium and Chasmanthium laxum clustered into a separate clade with the closest affinity to the clade comprising Zeugites pittieri Hack and Lophatherum gracile Brongn. In conclusion, our study describes the complete chloroplast genome of Chasmanthium latifolium for the first time, contributing to a better understanding of its taxonomy and evolution.

Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome

BACKGROUND/OBJECTIVES

Mitochondrial genomes are widely used in phylogenetics and evolutionary and ecological research.

METHODS

In this study, the newest mitochondrial genome of Chelonoidis vicina was assembled and annotated. The comparative mitochondrial genome and selection pressure analyses were used to examine the terrestrial adaptive evolution characteristics of C. vicina and other terrestrial reptiles.

RESULTS

The results reveal that the mitochondrial genome of the tortoise C. vicina is consistent with that of other tortoise species, comprising 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs, and 1 noncoding control region (CR). The analysis of selection pressure reveals the presence of positive selection sites in the COX2, COX3, Cytb, ND3, ND4, ND4L, ND5, and ND6 genes of terrestrial reptiles. Of these, the COX2 and ND3 genes exhibited faster evolutionary rates. The mitochondrial genome structure of C. vicina is consistent with that of different terrestrial reptiles. The positive selection sites of COX2 and ND3 in terrestrial reptiles are closely related to a change in mitochondrial energy metabolism, which is possibly related to terrestrial adaptability.

CONCLUSIONS

The results of this study provide new insights into the adaptive evolution of C. vicina to terrestrial niches from a mitogenomic perspective, as well as genetic resources for the protection of C. vicina.

The First Complete Chloroplast Genome Sequence of Secale strictum subsp. africanum Stapf (Poaceae), the Putative Ancestor of the Genus Secale

Secale strictum ssp. africanum (synonym Secale africanum), a putative ancestor of the genus Secale, has been classified within Secale strictum, although recent phylogenetic studies suggest that it represents a distinct species. This study reports the first complete chloroplast genome of S. africanum, highlighting its structure, genetic composition, and phylogenetic relationships within Secale and related Triticiceae species. Phylogeny reconstruction based on the maximum-likelihood method reveals notable genetic similarity between S. strictum and S. africanum, supporting their genetic and phylogenetic distinction. Here, we assembled the complete, annotated chloroplast genome sequence of Secale strictum ssp. africanum. The genome is 137,068 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number OQ700974. This work sheds light on the evolutionary history of Secale and contributes to our understanding of chloroplast genomics in cereal ancestors, with potential applications in improving cereal crop resilience, advancing breeding strategies, and informing conservation efforts for genetic diversity.

Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata

BACKGROUND

The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia.

RESULTS

In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection.

CONCLUSIONS

The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae.

Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China

BACKGROUND

Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo's persistence.

RESULTS

Analysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin's role as both glacial refugium and corridor for population expansion. Ancient trees (314-784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns.

CONCLUSIONS

Our findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo's evolution and informs conservation strategies for this endangered species.

Comprehensive analysis of the multi-rings mitochondrial genome of Populus tomentosa

BACKGROUND

Populus tomentosa, known as Chinese white poplar, is indigenous and distributed across large areas of China, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. However, limited accessibility to the mitochondrial (mt) genome of P. tomentosa impedes phylogenetic and population genetic analyses and restricts functional gene research in Salicaceae family.

RESULTS

Single-molecule real-time (SMRT) sequencing technology was used to sequence, assemble, and annotate the mt genome of P. tomentosa. This genome has a complex structure composed of four circular molecules ranging from 153,004 to 330,873 base pairs (bp). Each of these four circular molecules contains unique gene sequences that constitute the mt genome of P. tomentosa. The mt genome comprises 69 functional genes, including 38 protein-coding genes (PCGs), 26 tRNA genes, and 5 rRNA genes. After removing duplications, 19 different tRNA coding genes remain, though only 10 amino acids can be recognized. The noncoding region constitutes 93.38% of the mt genome, comprising a large number of repetitive sequences, gene spacer regions, and insertion from chloroplast sequences. Specifically, 40 chloroplast-derived sequences, with a total length of 24,381 bp, were identified in P. tomentosa.

CONCLUSIONS

In the current study, the results provide mitochondrial genomic evidence for the maternal origin of P. tomentosa and enhance understanding of the gene dialog between organelle genomes, contributing to the conservation and utilization of the genetic resources of P. tomentosa.

Phylogenetic and Comparative Genomics Study of Cephalopina titillator Based on Mitochondrial Genomes

Camel bot fly (Cephalopina titillator) larvae cause myiasis in domesticated and wild camels, resulting in significant economic losses to the camel industry and posing a serious global public health concern. To date, only one mitochondrial genome (mitogenome) of C. titillator isolated from the Alxa Bactrian camel has been reported. Herein, C. titillator was isolated from the Junggar Bactrian camel to assemble a complete circular mitogenome with a length of 16,552 bp encoding 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The mitogenome showed a high A + T content (73.31%), positive AT-skew (0.12), and negative GC-skew (-0.34) base composition patterns. All protein-coding genes (PCGs) employed ATG, ATA, ATT, GTG, or TCG as the start codons and TAA, TAG, or single T as the stop codons. Similar to other parasites in the Oestridae subfamily, the mitogenome was structurally conserved, with genes retaining the same order and direction as those in the ancestral insect mitogenome. The phylogenetic analysis clustered this species with the Oestrinae, showing that the subfamily did not exhibit monophyly. C. titillator isolated from the Junggar Bactrian camel was found to be a sister lineage to that isolated from the Alxa Bactrian camel. Despite the lack of data on the mitogenome of C. titillator isolated from dromedaries in the Middle East, phylogenetic analysis of C. titillator isolated from Xinjiang revealed one distinct lineage of the Xinjiang camel nasal bot fly. In conclusion, this study reports the complete mitogenome of Xinjiang C. titillator for the first time, providing valuable data for future studies on the phylogenetic relationships in this subfamily.

Comparative analysis of the complete chloroplast genome of Pueraria provides insights for species identification, phylogenetic relationships, and taxonomy

BACKGROUND

Pueraria is an edible and medicinal raw material, which is of great value to the pharmaceutical and food industries. Nonetheless, due to morphological diversity and complex domestication history, the classification of Pueraria plants is ambiguous. As the varieties on the market are mixed, the species are difficult to distinguish, and their morphological characteristics are similar to the physical and chemical properties. It is difficult to accurately identify them by traditional identification methods. Chloroplast (cp) genomes are widely used in species identification and phylogenetic studies to achieve accurate identification of medicinal plants, and can also provide more reference information for phylogenetic studies. Based on interspecific and intraspecific sampling, the cp genomes of eight species or varieties of Pueraria plants were examined in this study.

RESULTS

The study unveiled that the cp genome size varied from 151,555 to 153,668 base pairs (bp), with the total GC content ranging from 35.4 to 37.0%. Moreover, it was discerned that the cp genome contained between 128 and 135 genes. Comparative analysis indicated that the highest number of Simple Sequence Repeats (SSRs) was identified in P. montana and P. alopecuroides, with a preponderance of these SSRs being rich in Adenine (A) and Thymine (T) nucleotides. Complete comparison and sliding window analysis of the cp genome established that the non-coding region exhibited greater sequence differences than the coding region, and that the large single copy (LSC) region demonstrated higher nucleotide polymorphism levels. Fourteen highly variable loci such as rpoB,ycf1,rbcL,trnF-GAA-trnL,psbC-psbD, and ycf4-cemA were detected as potential molecular markers for Pueraria species identification. Moreover, the phylogenetic tree demonstrated that other Pueraria species had the most distant relationship with Haymondia wallichii and Toxicopueraria peduncularis, thereby offering fresh perspectives into the species classification of Pueraria. The molecular clock analysis results indicate that the divergence time of Pueraria may occur at ∼6.46 Ma. It is speculated that the cold climate may be the cause of Pueraria species diversity and promote the radiation of the genus.

CONCLUSION

This research provides theoretical backing and serves as a reference point for the identification and taxonomical classification of Pueraria species. The findings will prove beneficial in future studies on the preservation of medicinal resources, phylogenetic relationships, and genetic engineering of Pueraria plants.

Comparative and Adaptive Analyses of the Complete Chloroplast Genome Diversity in Sium serra

BACKGROUND/OBJECTIVES

Sium serra is distributed in Korea, China, and Japan. It was first identified as the genus Pimpinella and then reclassified as Sium by Kitagawa. Some Sium species are used as herbal medicine and are often confused with the similar form Ligusticum sinense. In this study, we analyzed the cp genome of S. serra and conducted comparative analyses with the cp genomes of related taxa.

METHODS

We extracted gDNA from fresh leaves and sequenced it using Illumina HiSeq2500. For the chloroplast genome assembly, de novo assembly was performed using Velvet v1.2.07. For the annotation, GeSeq and NCBI BLASTN were used. Afterwards, related taxa were analyzed using programs such as DnaSP and MISA.

RESULTS

S. serra was excluded from the study on the chloroplast (cp) genome in Sium because it was classified as Pimpinella in China. Therefore, this study aimed to analyze the cp genome of S. serra for the first time and its location within the genus Sium. The complete cp genome of S. serra was 154,755 bp in length, including a pair of inverted repeats, each 26,255 bp, a large single-copy region of 84,581 bp, and a small single-copy region of 17,664 bp. The cp genome comprised 79 protein-coding, 30 tRNA, and 4 rRNA genes. Furthermore, six regions of high nucleotide diversity were identified in the genus Sium. In the genus Sium, 1630 repeats that can serve as markers were also identified. Eight protein-coding genes with high KA/KS values were under positive selection in the Sium. Our phylogenetic analyses suggest that S. serra was positioned with high bootstrap support within the Sium of the tribe Oenantheae, specifically in the southern Palearctic subclade.

CONCLUSIONS

In this study, the S. serra chloroplast genome was sequenced and assembled. The genus Sium formed a monophyletic group; however, as not all the Sium species were included in this study, further research is necessary. This study can serve as foundational data not only for Sium but also for the tribe Oenantheae.

Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species

BACKGROUND

The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences.

RESULTS

The Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 - 98,561 bp), a small single copy (SSC, 14,172 - 21,575 bp), and a pair of inverted repeats (IRs, 26,225 - 35,204 bp). The genomes contain 108 - 113 unique genes, including 76 - 79 protein-coding genes, 28 - 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei, A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri 'zhuyajin1', Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade.

CONCLUSIONS

The genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus.

Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan

BACKGROUND

Tulipa species are economically, culturally, scientifically, and ecologically important. Tulips present taxonomic complexities that cannot be adequately resolved by examining their morphological characteristics alone or by relying on a limited selection of genetic markers.

METHODS

In the present study, we assessed the complete plastid sequences of Tulipa alberti Regel and Tulipa greigii Regel collected from Kazakhstan. Additionally, 14 previously published plastomes were obtained from GenBank for comparison and phylogenetic analysis.

RESULTS

The plastid genome sizes of T. alberti and T. greigii were 152,359 bp and 152,242 bp, respectively. In the plastid genomes of T. alberti and T. greigii, 136 genes were annotated, 114 of which were unique. These unique genes comprised eighty protein-coding, thirty transfer RNA, and four ribosomal RNA genes. Additionally, 415 simple sequence repeats were identified, comprising 107 tandem, 40 forward, 49 palindromic, 8 reverse, and 1 complementary repeat. Notably, the region containing ycf1 exhibited high variability and may serve as an informative DNA barcode for this genus.

CONCLUSION

Phylogenetic analysis showed strong support for the relationships among Tulipa species, indicating the utility of plastid genome data for further taxonomic studies within the genus.

Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae)

BACKGROUND

Capsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear.

RESULTS

The cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281-306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another.

CONCLUSIONS

This study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

Morphology, phylogeny, and mitogenomics reveal a new entomopathogenic fungus, Blackwellomyces changningensis (Hypocreales, Clavicipitaceae), from southwestern China

Two species of Blackwellomyces (Clavicipitaceae, Hypocreales, Ascomycota) were discovered during an investigation of the diversity of entomopathogenic fungi. A new fungus and one known fungal species that were gathered from Yunnan Province were described in this study. Blackwellomyces changningensis, sp. nov. was described using morphology and phylogenetic evidence from 14 mitochondrial protein-coding gene (PCG) data sets (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad5, nad6, and nad4L) and six nuclear genes (ITS [ITS4 and ITS5], 18S nuc rDNA [18S], 28S nuc rDNA [28S], tef1-α, rpb1, and rpb2). B. changningensis were found parasitic to Lepidoptera larvae and to produce filiform ascospores with septations. The asexual conidia were ovoid to ellipsoid in shape. Phylogenetic analysis and morphological observations concurred that the fungus belonged to a different species within the genus of Blackwellomyces. The foundation for further taxonomic, genetic, and evolutionary biological studies of the genus Blackwellomyces was laid by this work.

Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

BACKGROUND

Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.

RESULTS

We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259-155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.

CONCLUSIONS

The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.

Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes

Pears constitute an essential temperate crop and are primarily produced through interspecific hybridization owing to self-incompatibility that complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus and one Malus species using the Illumina HiSeq4000 platform. The cp genomes ranged from 159,885 bp to 160,153 bp and exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding, 36 tRNA, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in the coding regions and notable variations in the non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five intron-containing genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in the inverted repeat regions, while trnL-UAA was located in the large single-copy region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in the rpl22, petB, clpP, ndhA, and rps16 genes and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions Doonggeullebae and Cheongdangrori showed intron-length polymorphisms despite being classified as the same species. Phylogenetic analysis of the cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution as well as aiding in the conservation and breeding of pear germplasm.

Assembly and comparative analysis of the first complete mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria): insights into its genetic architecture and evolutionary relationships

Introduction

Zicaitai (Brassica rapa var. purpuraria) is a Brassica variety renowned for its distinctive taste and rich nutritional profile. In recent years, the mitochondrial genomes of several Brassica species have been documented, but the mitogenome of Zicaitai remains unreported.

Methods

In this study, we characterized the Zicaitai mitogenome achieved through the assembly of sequencing reads derived from both the Oxford Nanopore and Illumina platforms. A detailed comparative analysis was carried out with other Brassica species to draw comparisons and contrasts. In-depth analyses of codon usage patterns, instances of RNA editing, and the prevalence of sequence repeats within the mitogenome were also conducted to gain a more nuanced understanding of its genetic architecture. A phylogenetic analysis was performed, utilizing the coding sequences (CDS) from the mitochondrial genome of Zicaitai and that of 20 closely related species/varieties to trace evolutionary connections.

Results

The Zicaitai mitogenome is characterized by a circular structure spanning 219,779 base pairs, and it encompasses a total of 59 genes. This gene set includes 33 protein-coding genes, 23 tRNA genes, and 3 rRNA genes, providing a rich foundation for further genomic study. An analysis of the Ka/Ks ratios for 30 protein-coding genes shared by the mitogenomes of Zicaitai and seven other Brassica species revealed that most of these genes had undergone purifying selection. Additionally, the study explored the migration of genes between the chloroplast and nuclear genomes and the mitogenome, offering insights into the dynamics of genetic exchange within the Brassica genus.

Discussion

The collective results in this study will serve as a foundational resource, aiding future evolutionary studies focused on B. rapa, and contributing to a broader understanding of the complexities of plant evolution.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985 bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Comparative study on chloroplast genome of Tamarix species

Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non-SSR-related indels and 681 non-indel-related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single-copy and noncoding regions. The trnF-ndhJ, ndhC-trnM-CAU, ycf1, and trnL-UAG-ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

Comparative analyses of plastomes in Allaeanthus and Malaisia: structure, evolution, and phylogeny

The small genera Allaeanthus and Malaisia within the Moraceae have important edible, medicinal, and economic value. However, complete plastome blueprints and a well-resolved evolutionary history of these two genera are still lack, thereby limiting their conservation and application. The recent discovery of a new distribution of Allaeanthus kurzii in Hainan, China, marked by the collection of two unique samples, alongside three samples of Malaisia scandens, has opened new avenues for research. This study aimed to compare the Allaeanthus and Malaisia plastomes of Hainan Province samples with those of samples from other regions, focusing on plastome structure, codon usage bias, natural selection, and the evolutionary history of A. kurzii and M. scandens. The results showed that both species had a quadripartite plastome structure, with sizes ranging from 162,134 to 162,170 bp for A. kurzii and 161,235 to 162,134 bp for M. scandens. Both species displayed loss of the infA gene and reduction of the rpl22 gene. Two highly variable regions (petD-trnD-GUC and rpl20-clpP) and three highly variable genes (rpl20, petB, and rpl16) were identified in A. kurzii, while two highly variable regions (ycf2-ndhB and ccsA-ndhE) and three highly variable genes (psbT, rpl36, and ycf2) were found in M. scandens. The protein-coding sequences (CDSs) of the Allaeanthus and Malaisia plastomes exhibited similar patterns of adaptive indices and codon usage frequencies. The genes associated with photosynthesis underwent strong purifying selection. Phylogenetic analysis revealed that Allaeanthus, Broussonetia, and Malaisia constituted a monophyletic group, with Malaisia being more closely related to Broussonetia. Broussonetia diversified approximately 19.78 million years ago, Malaisia approximately 4.74 million years ago, and Allaeanthus approximately 16.18 million years ago. These new plastome-based discoveries will guide conservation planners and medicinal plant breeders and genetic resource development for these species in the region.

Analysis of codon usage patterns in complete plastomes of four medicinal Polygonatum species (Asparagaceae)

Polygonati Rhizoma and Polygonati odorati Rhizoma, known as "Huangjing" and "Yuzhu" in China, are medicinal Polygonatum species resources with top-grade medical and edible properties. The chloroplast (cp) genome has been used to study species diversity, evolution, and breeding of species for applications in genetic engineering. Codon usage bias (CUB), a common and complex natural phenomenon, is essential for studies of codon optimization of exogenous genes, genetic engineering, and molecular evolution. However, the CUB of medicinal Polygonatum species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal Polygonatum species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal Polygonatum species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal Polygonatum species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal Polygonatum species chloroplast genomes, and the preference to use AT-ending codons was observed in these species chloroplast genomes. The neutrality plot, ENC plot, PR2-Bias plot, and correspondence analysis showed that compared with mutation pressure, natural selection was the most important factor of CUB. Based on the comparative analysis of high-frequency codons and high expression codons, we also determined the 10-11 optimal codons of investigative medicinal Polygonatum species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal Polygonatum species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal Polygonatum species chloroplast genomes.

Complete mitochondrial genome and phylogenetic analysis of Mancinella alouina

BACKGROUND

The Muricidae family in the Class Gastropoda comprises numerous species with a vast range of morphological features and a worldwide presence. The phylogeny of the Muricidae has been analyzed in previous studies; however, the evolutionary relationships among the main branches of the Muricidae remain unknown.

METHODS AND RESULTS

In the present study, the mitochondrial genome of Mancinella alouina was sequenced. The mitochondrial genome was found to be 16,671 bp in length and made up of 37 genes (13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes). The genome has an A-T-rich region (66.5% A + T content) and all of the PCGs use the ATN start codon and the TAG or TAA stop codons. The mitochondrial gene arrangement of Mancinella alouina is similar to that of other Muricidae, except for Ocinebrellus inornatus and Ceratostoma burnetti. On the basis of a flexible molecular clock model, time-calibrated phylogenetic results indicate that the genus Mancinella diverged roughly 18.09 Mya, and that the family Muricidae emerged in the Late Cretaceous.

CONCLUSIONS

This study reveals the structural and sequence information features of the mitochondrial genome of Mancinella alouina. This study provides evidence for the relationships within the family Muricidae at the molecular level, and infer the divergence time. The results of phylogenetic analyses strongly support the current classification.

Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny

In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management.

Comparative analysis of chloroplast genome and evolutionary history of Hemerocallis

Members of the genus Hemerocallis have significant value as ornamental, edible, and medicinal plants, particularly in China, where they have been utilized for thousands of years as both a vegetable and Traditional Chinese Medicine. Hemerocallis species exhibit strict control over flowering time, with individuals flowering either diurnally or nocturnally. However, our understanding of the evolutionary history of this genus, especially concerning important horticultural traits, remains limited. In this study, sequencing and assembly efforts were conducted on 73 samples within the Hemerocallis genus. All accessions were classified into two distinct groups based on their diurnal (daylilies) or nocturnal (nightlilies) flowering habits. Comparative analysis of the chloroplast genomes from these two groups identified fifteen variant hotspot regions, including fourteen SNPs and one deletion, which hold promise for the development of molecular markers for interspecific identification. Phylogenetic trees, generated through both maximum-likelihood and Bayesian inference methods using 76 shared protein-coding sequences, revealed that diurnal flowering evolved prior to nocturnal flowering. The divergence between the two groups is estimated to have occurred approximately 0.82 MYA (95% CI: 0.35-1.45 MYA). The ancestral state of Hemerocallis is hypothesized to have featured diurnal flowering with orange yellow petals. This study marks the first reconstruction of the evolutionary history and ancestral state of the genus Hemerocallis. The findings contribute significantly to our understanding of the adaptation and speciation history within the genus.

Complete Plastid Genome Sequences of Four Salsoleae s.l. Species: Comparative and Phylogenetic Analyses

The taxonomic classification of the genera Salsola L., Pyankovia Akhani and Roalson, and Xylosalsola Tzvelev within Chenopodiaceae Vent. (Amaranthaceae s.l.) remains controversial, with the precise number of species within these genera still unresolved. This study presents a comparative analysis of the complete plastid genomes of S. foliosa, S. tragus, P. affinis, and X. richteri species collected in Kazakhstan. The assembled plastid genomes varied in length, ranging from 151,177 bp to 152,969 bp for X. richteri and S. tragus. These genomes contained 133 genes, of which 114 were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Thirteen regions, including ndhC-ndhD, rps16-psbK, petD, rpoC2, ndhA, petB, clpP, atpF, ycf3, accD, ndhF-ndhG, matK, and rpl20-rpl22, exhibited relatively high levels of nucleotide variation. A total of 987 SSRs were detected across the four analyzed plastid genomes, primarily located in the intergenic spacer regions. Additionally, 254 repeats were identified, including 92 tandem repeats, 88 forward repeats, 100 palindromic repeats, and only one reverse repeat. A phylogenetic analysis revealed clear clustering into four clusters corresponding to the Salsoleae and Caroxyloneae tribe clades. These nucleotide sequences obtained in this study represent a valuable resource for future phylogenetic analyses within the Salsoleae s.l. tribe.

Camellia neriifolia and Camellia ilicifolia (Theaceae) as separate species: evidence from morphology, anatomy, palynology, molecular systematics

BACKGROUND

The systematic status of sect. Tuberculata and its taxonomy have recently attracted considerable attention. However, the different bases for defining the characteristics of sect. Tuberculata has led to many disagreements among the plants in this group. Camellia neriifolia and Camellia ilicifolia have been the subject of taxonomic controversy and have been treated as different species or varieties of the same species. Therefore, it is important to use multiple methods, i.e., integrative taxonomy, to determine the taxonomic status of C. neriifolia and C. ilicifolia. This is the first study to systematically explore the taxonomic position of these two plants on the basis of Morphology, Anatomy, Palynology and Molecular Systematics.

RESULTS

Extensive specimen reviews and field surveys showed that many differences exist in C. neriifolia and C. ilicifolia, such as the number of trunk (heavily debarked vs. slightly peeling), leaf type (smooth thin leathery, shiny vs. smooth leathery, obscure or slightly shiny), leaf margin (entire vs. serrate), flower type (subsessile vs. sessile), number of styles (3-4 vs. 3), and sepal (ovate vs. round). Moreover, C. neriifolia has a more distinctive faint yellow flower color, and trunk molting was more severe in C. neriifolia than that in C. ilicifolia. In addition, micromorphological analysis of the leaf epidermis showed that the two species differed in the anticlinal wall, stomatal apparatus, and stomatal cluster, and pollen morphology analyses based on pollen size, germination furrow, and polar and equatorial axes showed that they are both distinct from each other. The results of the phylogenetic tree constructed based on the whole chloroplast genome, protein-coding genes, and ITS2 showed that both C. ilicifolia and C. neriifolia were clustered in different branches and gained high support.

CONCLUSIONS

The results combine morphology, anatomy, palynology, and molecular systematics to treat both C. neriifolia and C. ilicifolia as separate species in the sect. Tuberculata, and the species names continue to be used as they were previously. In conclusion, clarifying the taxonomic status of C. neriifolia and C. ilicifolia deepens our understanding of the systematic classification of sect. Tuberculata.

Comparative Analysis of Plastome Sequences of Seven Tulipa L. (Liliaceae Juss.) Species from Section Kolpakowskianae Raamsd. Ex Zonn and Veldk

Tulipa L. is a genus of significant economic, environmental, and cultural importance in several parts of the world. The exact number of species in the genus remains uncertain due to inherent taxonomic challenges. We utilized next-generation sequencing technology to sequence and assemble the plastid genomes of seven Tulipa species collected in Kazakhstan and conducted a comparative analysis. The total number of annotated genes was 136 in all seven studied Tulipa species, 114 of which were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Nine regions (petD, ndhH, ycf2-ycf3, ndhA, rpl16, clpP, ndhD-ndhF, rpoC2, and ycf1) demonstrated significant nucleotide variability, suggesting their potential as molecular markers. A total of 1388 SSRs were identified in the seven Tulipa plastomes, with mononucleotide repeats being the most abundant (60.09%), followed by dinucleotide (34.44%), tetranucleotide (3.90%), trinucleotide (1.08%), pentanucleotide (0.22%), and hexanucleotide (0.29%). The Ka/Ks values of the protein-coding genes ranged from 0 to 3.9286, with the majority showing values <1. Phylogenetic analysis based on a complete plastid genome and protein-coding gene sequences divided the species into three major clades corresponding to their subgenera. The results obtained in this study may contribute to understanding the phylogenetic relationships and molecular taxonomy of Tulipa species.

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BACKGROUND

Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.

RESULTS

Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.

CONCLUSIONS

The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species

Bromus (Poaceae Bromeae) is a forage grass with high adaptability and ecological and economic value. Here, we sequenced Bromus ciliatus, Bromus benekenii, Bromus riparius, and Bromus rubens chloroplast genomes and compared them with four previously described species. The genome sizes of Bromus species ranged from 136,934 bp (Bromus vulgaris) to 137,189 bp (Bromus ciliates, Bromus biebersteinii), with a typical quadripartite structure. The studied species had 129 genes, consisting of 83 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The highest GC content was found in the inverted repeat (IR) region (43.85-44.15%), followed by the large single-copy (LSC) region (36.25-36.65%) and the small single-copy (SSC) region (32.21-32.46%). There were 33 high-frequency codons, with those ending in A/U accounting for 90.91%. A total of 350 simple sequence repeats (SSRs) were identified, with single-nucleotide repeats being the most common (61.43%). A total of 228 forward and 141 palindromic repeats were identified. No reverse or complementary repeats were detected. The sequence identities of all sequences were very similar, especially with respect to the protein-coding and inverted repeat regions. Seven highly variable regions were detected, which could be used for molecular marker development. The constructed phylogenetic tree indicates that Bromus is a monophyletic taxon closely related to Triticum. This comparative analysis of the chloroplast genome of Bromus provides a scientific basis for species identification and phylogenetic studies.

The complete mitochondrial genome of Zaomma eriococci (hymenoptera: encyrtidae)

The complete mitochondrial genome of the Zaomma eriococci (Ferrière, 1955) (Hymenoptera: Encyrtidae) was obtained through next-generation sequencing, making the first reported complete mitochondrial genome of the genus Zaomma. The mitochondrial genome is 15,648 bp in length and includes 37 classical eukaryotic mitochondrial genes along with an A + T rich region. All 13 protein-coding genes (PCGs) initiate with typical ATN codons. Of these, 10 PCG genes terminate with TAA, while three terminate with TAG. Additionally, there are 22 tRNA genes, ranging in size from 62 to 70 bp. The maximum likelihood phylogenetic tree was constructed based on 13 PCGs, indicates that Z. eriococci is closely related to Tassonia gloriae. This mitochondrial genome will serve as a valuable molecular resource for species identification, genetic analysis, and comparative genomic studies of Z. eriococci, contributing to the growing collection of mitochondrial genomes within the family Encyrtidae.

Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis

The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.

Plastid phylogenomics contributes to the taxonomic revision of taxa within the genus Sanicula L. and acceptance of two new members of the genus

Introduction

The genus Sanicula L. is a taxonomically complicated taxa within Apiaceae, as its high variability in morphology. Although taxonomists have performed several taxonomic revisions for this genus, the interspecific relationships and species boundaries have not been satisfactorily resolved, especially for those endemic to China. This study mainly focused on S. giraldii var. ovicalycina, S. tienmuensis var. pauciflora, and S. orthacantha var. stolonifera and also described two new members of the genus.

Methods

We newly sequenced sixteen plastomes from nine Sanicula species. Combined with eleven plastomes previously reported by us and one plastome downloaded, we performed a comprehensively plastid phylogenomics analysis of 21 Sanicula taxa.

Results and Discussion

The comparative results showed that 21 Sanicula plastomes in their structure and features were highly conserved and further justified that two new species were indeed members of Sanicula. Nevertheless, eleven mutation hotspot regions were still identified. Phylogenetic analyses based on plastome data and the ITS sequences strongly supported that these three varieties were clearly distant from three type varieties. The results implied that these three varieties should be considered as three independent species, which were further justified by their multiple morphological characters. Therefore, revising these three varieties into three independent species was reasonable and convincing. Moreover, we also identified and described two new Sanicula species (S. hanyuanensis and S. langaoensis) from Sichuan and Shanxi, China, respectively. Based on their distinct morphological characteristics and molecular phylogenetic analysis, two new species were included in Sanicula. In summary, our study impelled the revisions of Sanicula members and improved the taxonomic system of the genus.

Impatiensyingjingensis (Balsaminaceae), a new species from Sichuan, China

This study describes Impatiensyingjingensis X.Q. Song, B.N. Song & Biao Yang, sp. nov., a new species collected from the Yingjing area of the Giant Panda National Park. This new species is distributed at an altitude of 1400-2100 m, with a plant height of 30-130 cm. The flowers are purple-red or light purple red, with 3-9 flowers on each inflorescence and the dorsal auricle of the lateral united petals is thread-like and about 2 cm long, differing significantly from other species of Impatiens. Furthermore, molecular data, as well as micro-morphological evidence under SEM (of pollens), also support the establishment of the new species.

A comparative plastome approach enhances the assessment of genetic variation in the Melilotus genus

BACKGROUND

Melilotus, a member of the Fabaceae family, is a pivotal forage crop that is extensively cultivated in livestock regions globally due to its notable productivity and ability to withstand abiotic stress. However, the genetic attributes of the chloroplast genome and the evolutionary connections among different Melilotus species remain unresolved.

RESULTS

In this study, we compiled the chloroplast genomes of 18 Melilotus species and performed a comprehensive comparative analysis. Through the examination of protein-coding genes, we successfully established a robust phylogenetic tree for these species. This conclusion is further supported by the phylogeny derived from single-nucleotide polymorphisms (SNPs) across the entire chloroplast genome. Notably, our findings revealed that M. infestus, M. siculus, M. sulcatus, and M. speciosus formed a distinct subgroup within the phylogenetic tree. Additionally, the chloroplast genomes of these four species exhibit two shared inversions. Moreover, inverted repeats were observed to have reemerged in six species within the IRLC. The distribution patterns of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within protein-coding genes indicated that ycf1 and ycf2 accumulated nonconservative alterations during evolutionary development. Furthermore, an examination of the evolutionary rate of protein-coding genes revealed that rps18, rps7, and rpl16 underwent positive selection specifically in Melilotus.

CONCLUSIONS

We present a comparative analysis of the complete chloroplast genomes of Melilotus species. This study represents the most thorough and detailed exploration of the evolution and variability within the genus Melilotus to date. Our study provides valuable chloroplast genomic information for improving phylogenetic reconstructions and making biogeographic inferences about Melilotus and other Papilionoideae species.

Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number

The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.

Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)

Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.

Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence

BACKGROUND

Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences.

RESULTS

We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat.

CONCLUSIONS

Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.