Comparative Analyses of Six Complete Chloroplast Genomes from the Genus Cupressus and Juniperus (Cupressaceae)

Comparative and phylogenetic analysis of Potentilla and Dasiphora (Rosaceae) based on plastid genome

BACKGROUND

Potentilla L. and Dasiphora L. are predominantly perennial herbs, occasionally manifesting as annuals or shrubs, primarily found in the northern temperate zone. However, taxonomic classification within this group remains contentious, particularly regarding genus boundaries and species delineation. Therefore, this study sequenced and analyzed the complete plastid genomes of 19 species from Potentilla and Dasiphora, comparing them with five previously published plastid sequences. Our objectives included reconstructing phylogenetic relationships within Potentilla and Dasiphora and investigating cytonuclear discordance among them.

RESULTS

These plastid genomes were highly conserved in structure, GC content, and overall genome composition, comprising 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Notably, all Dasiphora plastid genomes lacked the unique intron for rpl2. Comparative genomic analyses revealed that variations in plastid genome size were due to differences in the lengths of the LSC, SSC, and IR regions. The IR region was predominantly conserved, while non-coding regions exhibited higher variability than coding regions. We screened SSR and identified seven highly variable loci that serve as potential molecular markers, offering valuable insights into the intergeneric relationships between Potentilla and Dasiphora. Phylogenetic analyses based on nuclear (ITS, ETS) and cytoplasmic (plastid, mitochondrial) genes confirmed the monophyly of Potentilla and Dasiphora, with results largely consistent with previous studies and supported by robust reliability metrics. We identified cytonuclear conflicts within Potentilla, which frequently disrupt its monophyly. We hypothesize that these conflicts may result from interspecific hybridization or incomplete lineage sorting events during the evolutionary history of the genus.

CONCLUSIONS

This study offers a theoretical foundation for advancing molecular identification and phylogenetic research on Potentilla and Dasiphora species. However, future work could benefit from greater detail on the criteria for selecting mitochondrial gene sequences and nrDNA datasets.

Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships of 21 Sect. Camellia (Camellia L.) Plants

Background: Section Camellia is the most diverse group in the genus Camellia L., and this group of plants has a long history of cultivation in China as popular ornamental flowers and oil plants. Sect. Camellia plants present diverse morphological variations and complexity among species, resulting in uncertainty in the classification of species, which has resulted in a degree of inconvenience and confusion in the use of plant resources and research. Methods: Here, We sequenced and assembled the chloroplast genomes of 6 sect. Camellia and performed comparative chloroplast genome analysis and phylogenetic studies combined with 15 existing sect. Camellia plants. Results: The chloroplast genome of 21 species in sect. Camellia species were quadripartite with length of 156,587-157,068 bp base pairs (bp), and a highly conserved and moderately differentiated chloroplast genome arrangement. The 21 sect. Camellia chloroplast genomes were similar to those of angiosperms, with high consistency in gene number, gene content and gene structure. After the annotation process, we identified a total of 132 genes, specifically 87 sequences coding for proteins (CDS), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The ycf1 gene in 21 species of the sect. Camellia was present only in the small single-copy/inverted repeat of a (SSC/IRa) region. Sequence variation was greater in the large single-copy (LSC) region than in the IR region, and the majority of the protein-coding genes presented high codon preferences. The chloroplast genomes of 21 plant species exhibit relatively conserved SC (single copy region)/IR (inverted repeat region) boundaries. We detected a total of 2975 single sequence repeats (SSRs) as well as 833 dispersed nuclear elements (INEs). Among these SSRs, A/T repeats and AT/AT repeats dominated, while among INEs, forward repeats and palindromic repeats predominated. Codon usage frequencies were largely similar, with 30 high-frequency codons detected. Comparative analysis revealed five hotspot regions (rps16, psaJ, rpl33, rps8, and rpl16) and two gene intervals (atpH-atpI and petD-rpoA) in the cp genome, which can be used as potential molecular markers. In addition, the phylogenetic tree constructed from the chloroplast genome revealed that these 21 species and Camellia oleifera aggregated into a single branch, which was further subdivided into two evolutionarily independent sub-branches. Conclusions: It was confirmed that sect. Camellia and C. oleifera Abel are closely related in Camellia genus. These findings will enhance our knowledge of the sect. Camellia of plants, deepen our understanding of their genetic characteristics and phylogenetic pathways, and provide strong support for the scientific development and rational utilization of the plant resources of the sect. Camellia.

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.

New Insights Into The Evolution of Chloroplast Genomes in Ochna Species (Ochnaceae, Malpighiales)

Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa.

Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis

The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.

Novel molecular markers for Taxodium breeding from the chloroplast genomes of four artificial Taxodium hybrids

Taxodium "Zhongshanshan" are a group of intraspecific Taxodium hybrids with superparental dominance and high ecological and economic value in southern China. Identifying the parentage of hybrids, especially the male parent, is critically important for genetic studies. However, the large nuclear genomes of members of the genus Taxodium pose a major challenge for the development of molecular markers. Here, we developed novel molecular markers by conducting a comparative analysis of the chloroplast genomes of four artificial Taxodium hybrids and their parents. The lengths of the whole chloroplast genome ranged from 131,942 to 132,128 bp, and the total guanine (GC) content of the chloroplast genomes ranged from 34.6% to 35.81%. A total of 120 unique genes were identified, including 83 protein-coding genes, 33 transfer RNAs, and four ribosomal RNAs. There were 69-71 simple sequence repeats were detected in the four hybrids. Phylogenetic analysis revealed that these hybrids clustered with their paternal parents. Similar findings were obtained by analysis of the GC content of protein-coding genes. Molecular markers were developed using the highly variable regions of the chloroplast genomes, and polymerase chain reaction (PCR) assays revealed that these markers were effective for identifying the male parents of these hybrids. Our findings indicate for the first time that the chloroplast genomes of Taxodium are paternally inherited. Generally, these molecular markers could facilitate breeding and genetic studies of Taxodium.

Environmental Factors Driving the Spatial Distribution Pattern of Venerable Trees in Sichuan Province, China

Venerable trees are important natural resources and cultural heritage, offering historical, ecological, social and economic value. However, global warming and anthropogenic activities have threatened their welfare and survival. A comprehensive understanding of their current and future spatial patterns, vis-á-vis environmental conditions, can inform the co-management of sustainable resource use and conservation. We employed the existing spatial occurrence data and environmental variables (bioclimate and elevation) to simulate the optimal habitats for venerable trees in China's Sichuan Province. We evaluated the current and future climate scenarios of 2100 with double CO₂ concentration. The BIOCLIM and QGIS spatial analyses assessed the primary factors of geographical distribution. The results identified 10,720 venerable trees from 123 species, 81 genera and 42 families. Cupressus funebris dominated, with the maximum importance value, followed by Ginkgo biloba, Ficus virens var. sublanceolata, and Phoebe zhennan. The elevation distribution of tree abundance and species richness demonstrated a unimodal pattern, skewing to the low-elevation end, with a concentration in the 600-1500 m low-medium altitude. The majority of trees and excellent habitats were found in eastern Sichuan with a less harsh terrain and climate. The bio3 (isothermality) and bio7 (temperature annual range) factors significantly influenced tree occurrence. Temperature imposed a greater effect on distribution than moisture under the current climate scenario. For the future climate-change scenario, the suitable habitats were predicted to maintain an overall stable pattern, with largely contiguous expansions of better habitats. However, climate warming would shrink the excellent habitats on the plains. The findings can inform strategies and guidelines for venerable-tree conservation in Sichuan. Furthermore, vulnerable areas could be identified. The future range expansion sites could be enlisted to cultivate new trees to replenish the venerable-tree pool. Habitat patches that remain sustainable could provide refugia with the potential for protected-area designation.