Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships

Xu, Ke‐Wang; Lee, Shiou Yih; Mao, Lingfeng; Meng, Kaikai

doi:10.1186/s12864-022-08397-9

Cited by 20 publications

(16 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the Eriocaulon chloroplast genomes, we found 33 to 58 SSR loci. Other studies have shown that the most abundant SSRs were A/T-rich mononucleotide repeats, which was consistent with the chloroplast genome's common polyA or polyT repeats and rare G or C repeats [35,[51][52][53]. Dinucleotide repeats were the most common type in the Eriocaulon chloroplast genomes (Table 2) and had high AT content.…”

Section: Chloroplast Genome Evolution Of Eriocaulonsupporting

confidence: 75%

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Liu

Deng

et al. 2023

BMC Plant Biol

View full text Add to dashboard Cite

Background Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. Results The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. Conclusion Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.

show abstract

Section: Chloroplast Genome Evolution Of Eriocaulonsupporting

confidence: 75%

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Liu

Deng

et al. 2023

BMC Plant Biol

View full text Add to dashboard Cite

show abstract

“…Highly variable regions provide abundant phylogenetic information and can be used as potential molecular markers to delimit closely related taxa [ 55 ]. The Pi of highly variable regions within subgenus Gynopodium species was lower (< 0.008) compared with previously published values of other species [ 56 , 57 ] and some of Magnolia species [ 29 , 30 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Xie

Zhang

et al. 2022

BMC Genomics

View full text Add to dashboard Cite

Background The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. Results The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). Conclusion The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

show abstract

“…in China) are widely grown in parks and gardens throughout the world for their foliage and decorative berries (e.g., on Christmas trees) and hold an important position in gardens worldwide. However, genetic research on holly species has mainly focused on evaluating their genetic diversity by identifying molecular markers, determining phylogenetic relationships, and revealing speciation and lineage diversification until now (Gottlieb et al, 2005;Selbach-Schnadelbach et al, 2009;Manen et al, 2010;Shi et al, 2016;Xu et al, 2021;Yao et al, 2021). The weak foundation of genome-wide research not only for the entire family Aquifoliaceae but also for the order Aquifoliales is not equal to the importance of these groups.…”

Section: Introductionmentioning

confidence: 99%

The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change

Wei

Zhang

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.

show abstract

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships

Cited by 20 publications

References 72 publications

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change

Contact Info

Product

Resources

About