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Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F . sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 ( F . dinganensis and F . howii ) to 190 ( F . polynervis ), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes ( accD , clpP , ndhK , rbcL , rpl20 , rpl22 , rpl23 , rpoC1 , rps15 , and rps4 ) which exhibited potential positive selective signatures. Five hypervariable genic regions ( rps15 , ycf1 , rpoA , ndhF , and rpl22 ) and five hypervariable intergenic regions ( trnH-GUG - psbA , rpl32 - trnL-UAG , psbZ - trnG-GCC , trnK-UUU - rps 16 and ndhF - rpl32 ) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus , despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F . sarmentosa complex and F . auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

Figs are keystone resources of tropical and subtropical forests since they are speciose and supporting plenteous animals. Ficus sarmentosa var. henryi (King) Corner, a functionally dioecious evergreen fig, is threatened by habitat loss and fragmentation. However, genetic information has hitherto been nearly terra incognita for this species, which hinders the protection and management of this species and the forests. In this study, we developed and characterized 10 polymorphic microsatellites in F. sarmentosa var. henryi. The numbers of alleles per locus varied from 2 to 15. The observed and expected heterozygosities within populations were 0–0.857 and 0–0.876, respectively. These polymorphic microsatellites will contribute to further population genetic studies, and thereby benefit resource conservation and forest protection.

Ficus sarmentosa is a common climbing fig tree in East Asia in Moraceae, and its particular geographical distributed pattern and on-going radiation evolution make it significant to explore evolutionary history and biogeography of Ficus. In this work, the first complete chloroplast genome of F. sarmentosa was reported using Illumina NovaSeq high-throughput sequencing data. Totally, the whole chloroplast genome of F. sarmentosa is 160,183 bp in length, which includes large single-copy region of 88,307 bp, small single-copy region of 20,080 bp, and two pairs of inverted repeat regions of 25,898 bp. In addition, GC content and microsatellite makers of the genome were explored. Lastly, phylogenetic analysis demonstrated the closest relationship between F. sarmentosa and F. pumila.