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Comparative Analysis and Phylogenetic Investigation of Hong www.nature.com/scientificreports OPEN Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes Bobby Lim‑Ho Kong1,3, Hyun‑Seung Park2, Tai‑Wai David Lau1,3, Zhixiu Lin4, Tae‑Jin Yang2 & Pang‑Chui Shaw1,3* Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex gracilifora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein‑coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassifed; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refne its classifcation. Ilex, a monogeneric plant group in the family Aquifoliaceae, is a widespread genus. It can either be evergreen or deciduous and can be found throughout subtropical regions. Tere are approximately 600 species in total, and some of them have medical uses1. Some kinds of Ilex are commonly used herbs in traditional Chinese medicine (TCM), and they are efective in treating infuenza, relieving pain and anti-infammation2,3. Te mechanism has been recently proposed. Asprellcosides from I. asprella can signifcantly inhibit the replication of infuenza A virus, while rotundarpene from I. rotunda var. microcarpa can inhibit the TNF-α-mediated pathway 4,5. Ilex species have a variety of pharmacological properties, and accurate classifcation of them is needed. Cuénoud and colleagues used the rbcL and atp-rbcL spacer to study the phylogenetic relationship of Ilex. A total of 116 Ilex species were classifed into the American clade, Asian/North American clade, deciduous clade and Eurasian clade6. Manen and colleagues used both chloroplast markers and the 5S RNA spacer to assign 105 Ilex into the 4 clades. Afer that, Ilex was further assigned to diferent subgenera, sections and alliances7. Nuclear DNA ITS and nepGS were also included in recent research1. In addition to the commonly used DNA regions, Lin and colleagues have also used the nuclear segment gapC to study the speciation of Ilex8. According to Flora of China, Ilex can be divided into three subgenera, Byronia, Ilex and Prinos9. Tese three subgenera can be further classifed into taxonomic sections and series. Te classifcation was generally based on morphological analysis, and only short universal DNA markers of some species were included in the studies. Chloroplasts are responsible for multiple functions, such as photosynthesis10, amino acid synthesis and nitro- gen metabolism in plants11,12. As most DNA markers, such as rbcL, matK and psbA, are located in the chloroplast genome, the development of chloroplast whole-genome sequencing has contributed to solving the phylogenetic 1Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine and Institute of Chinese Medicine, The Chinese University of Hong Kong, ShatinHong Kong, N.T., China. 2Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea. 3Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, ShatinHong Kong, N.T., China. 4School of Chinese Medicine, The Chinese University of Hong Kong, ShatinHong Kong, N.T, China. *email: [email protected] Scientifc Reports | (2021) 11:5153 | https://doi.org/10.1038/s41598-021-84705-9 1 Vol.:(0123456789) www.nature.com/scientificreports/ relationship of plants13–15. In addition to classical DNA barcoding regions, novel DNA markers can also be found16. Here, we obtained the complete chloroplast genomes of 19 Ilex species native to Hong Kong. Divergence hotspot investigation, repeat analysis and polymorphism studies were performed. Trough including other published Ilex chloroplast genomes, topologies of the Ilex phylogenies were constructed. Results Chloroplast genome assembly. By using the Illumina NovaSeq 6000 system, the complete chloroplast genomes of 19 Ilex species were sequenced. Raw data were generated with an average read length of 150 bp. Complete chloroplast sequences were assembled by de novo assembly and validated by mapping the raw reads into the assembled contigs. Sequences of the reads and contigs were compared, and the fnal plastomes were sub- mitted to GenBank with accession numbers according to the supplementary material (Supplementary Table S1). Afer that, 19 Ilex genomes were used for indel, SSR and REPuter analyses. Te corresponding genome map of I. pubescens is shown as a reference (Fig. 1). Genome structure and gene content. Tese genomes followed the typical quadripartite structure of angiosperms, which consisted of one LSC Sect. (86,506–87,400 bp), one SSC Sect. (18,380–18,442 bp) and a pair of IR regions (26,065–26,125 bp). Te GC content ranged from 37.6% to 37.7%, which was consistent with a previous report of Ilex chloroplast genomes17–19. All of the 19 Ilex species have the same gene content and gene order. Tey contain 125 genes, of which 88 are protein-coding genes, 37 are tRNA genes and 8 are encode rRNA (Table 1). Seventeen genes contain one or more introns, of which 12 (ycf3, atpF, petB, petD, ndhA, ndhB, rpoC1, rps12, rps16, rpl2, rpl16, and clpP) are protein-coding, and fve are responsible for tRNA (trnA-UGC, trnI-GAU, trnL-UAA, trnQ-UUG, and trnV-UAC). Several genes are duplicated in the IR regions, among which 8 (ndhB, rps7, rps12, rpl2, rpl23, ycf1, ycf2, and ycf15) are protein coding, 7 (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC) encoded tRNAs, and 4 (rrn4.5, rrn5, rrn16, and rrn23) encode rRNA (Table 2). Only one pseudogene, ycf1, was found in all Ilex genomes. Tis observation was consistent with the seven Ilex genomes in Yao’s study 17. Te similarities in the genome structure and genetic content indicate that the chloroplast genomes of all 19 Ilex species are highly conserved. Simple and complex repeats analysis. Simple sequence repeats (SSRs) are repeating DNA motifs that range from one to six nucleotides20. Te number and position of repeated motifs are thought to be useful in population genetic studies and have been widely used in fnding polymorphisms in chloroplast genomes21,22. By using MISA analysis tools, the number and position of diferent SSR motifs in 19 Ilex were investigated. All of the Ilex species do not have penta-nucleotide motifs, while Ilex rotunda var. microcarpa is the only species containing hexa-nucleotide repeat motifs. Mono-nucleotide repeat motifs account for the largest proportion, ranging from 44 to 56 (Fig. 2a). Most of the mono-nucleotide repeat motifs are A/T repeats, while only 5 species, I. trifora, I. viridis, I. asprella var. tapuensis, I. cinerea and I. gracilifora, have C/G repeat motifs. A/T repeats occupy at least 75.9% of the total SSR, and the phenomenon of AT richness in the SSR of terrestrial plants has been reported in previous studies23,24. Te numbers and types of di-, tri- and tetra-nucleotide motifs are mostly conserved among Ilex, except for the ACAT/ATGT tetra-nucleotide motif, which is present only in I. fcoidea and I. pubescens (Supplementary Table S2). Regarding the SSR distribution, most of the SSRs are found in the LSC and SSC regions but not the IR regions, which is consistent with studies in angiosperms (Fig. 2b)25–27. Owing to the variation in the LSC, IR and SSC lengths, densities of SSRs in diferent regions were also calculated (Supplementary Table S3). Only a few SSRs were found in the two IR regions; therefore, only slight variation was observed in these regions. On the other hand, relatively large variation in the SSR density was noticed in the SSC regions, which varied from 1.63E−04 in I. cornuta to 4.35E-04 in I. trifora. Complex repeat regions are important in recombination and variation in chloroplast genomes28. By using the REPuter algorithm, complex repeats of Ilex were analysed. Te length of repeats is 30–66 bp, which falls into the typical range of other angiosperms29,30. Tere are only slight variations in the total number of repeats, which ranged from 19 to 26, but the number of each repeating motif is diferent. Te most abundant repeats are direct repeats, while palindromic repeats are secondary. Complementary repeats can be observed in only eight Ilex species, and reverse repeats can be seen only in fve Ilex species (Fig. 3). Te variation in the repeating motifs of SSRs and complex repeats can be used as DNA markers to identify these species. Interspecies comparison of chloroplast genomes. Single-nucleotide polymorphisms (SNPs) and DNA insertion-deletion mutations (indels) are important for discovering DNA markers and barcodes in medici- nal herbs31,32. Terefore, the number of SNPs and indels were calculated by pair-wise alignment of the 19 Ilex chloroplast genomes. In brief, the 19 Ilex genomes were frst aligned with each other. Te number of polymor- phisms was identifed by an in-house developed Perl algorithm.
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