Abstract
Atalantia plants are small trees in the family Rutaceae that have great potential for use in agriculture, medicine, and carving. However, the phylogenetic relationships of Atalantia species have not been systematically studied due to the lack of available molecular resources and highly variable molecular markers. In this study, the complete chloroplast genomes of four Atalantia species were newly sequenced and characterized. The length of the chloroplast genomes in Atalantia species ranged from 159,557 to 160,341 bp, which was more similar to Fortunella and Citrus species in the Rutaceae. The rpl22 genes were pseudogenized at the SSC/IRa boundary. Certain mechanisms have been evolved to compensate for the pseudogenization of the accD and infA genes in Atalantia chloroplast genomes. Some highly divergent intergenic regions (trnH-GUG–psbA, rps16–trnQ-UUG, trnS-GCU–trnG-UCC, atpF–atpI, petN–psbM, psbM–trnD-GUC, ndhC–trnV-UAC, atpB–rbcL, accD–psaI, and ycf4–cemA) and genes (psbM, trnD-GUC, rpl32, ndhF, and ycf1) were detected, which serve as potential phylogenetic markers. The phylogenetic relationships and divergence times of Atalantia species were explored based on the complete chloroplast genome. Based on the phylogenetic trees, Atalantia species were grouped into two sub-branches. Atalantia monophylla and A. buxifolia were found to be more closely related, whereas A. ceylanica and A. roxburghiana exhibited a closer relationship. The divergence time estimation indicated that the common ancestor of the Atalantia species diverged approximately 14.26 million years ago. These findings will help with the identification, categorization, and utilization of Atalantia species.
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Data availability
In the GenBank database, the data supporting the findings of this study can be found at https://www.ncbi.nlm.nih.gov/, under accession numbers NC_065396–NC_065399.
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Acknowledgements
This work was supported by the State Key Laboratory of Palaeobiology and Stratigraphy (Nos. 223123 and 213119), National Natural Science Foundation of China (No. 31801022), and Shandong Province Natural Science Foundation of China (No. ZR2019BC094).
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WBS helped in conceptualization, data curation, investigation, methodology, project administration, software, visualization, writing—review & editing, writing—original draft. WCS contributed to conceptualization, data curation, formal analysis, investigation, project administration. YZ was involved in data curation, formal analysis, validation. CS performed conceptualization, data curation, funding acquisition, project administration, supervision, writing—original draft. SW helped in data curation, funding acquisition, project administration. All authors contributed to the article and approved the submitted version.
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Online Resource 1. Taxonomic position, species name and NCBI accession numbers of Aurantioideae species in the phylogenetic trees.
Online Resource 2. The results of mapping the reads to the assembled Atalantia complete cp genome sequences.
Online Resource 3. The individual chloroplast genome maps for each Atalantia species.
Online Resource 4. Statistics on the relative synonymous codon usage (RSCU) values of different Atalantia species.
Online Resource 5. Statistics of Ka/Ks values obtained from selection pressure analysis of other Atalantia species, using Atalantia roxburghiana as a reference.
Online Resource 6. Statistics regarding the number, type, region, and location of simple sequence repeats (SSRs) in diverse Atalantia chloroplast genomes.
Online Resource 7. Statistics regarding the type, number, region, and location of long repeats in diverse Atalantia chloroplast genomes.
Online Resource 8. Statistics on the nucleotide diversity (Pi) values of the Atalantia chloroplast genome, as well as the corresponding gene regions and their locations.
Online Resource 9. The pseudogenization of the accD gene in A. kwangtungensis.
Online Resource 10. Information on heterozygous variants present in Atalantia species, including Phred-scaled quality scores, genotypes, and likelihood statistics for each genotype.
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Shi, W., Song, W., Zhao, Y. et al. Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation. Plant Syst Evol 309, 31 (2023). https://doi.org/10.1007/s00606-023-01868-w
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DOI: https://doi.org/10.1007/s00606-023-01868-w