Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Nov. 23, 2023

Abstract Background Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear chloroplast genomes of F. have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, genomic DNA yellowish leaf material was extracted, sequenced by using mixture Illumina Novaseq6000 short reads Oxford Nanopore PromethION long reads, sequencing data were assembled annotated. Result The obtained in length 535,692 bp with circular structure, GC content 44.90%. contains 60 genes, including 36 protein-coding 21 tRNA three rRNA genes. We further analyzed RNA editing relative synonymous codon usage, repeats based on data. There 25 homologous sequences between mitochondria genome, which involved transfer 8 9473 genomes. Analysis nucleic acid substitution rate, diversity, collinearity genes revealed that majority may undergone purifying selection, exhibiting slower rate evolution relatively conserved structure. phylogenetic relationships among different species most closely related Olea europaea subsp. Europaea. Conclusion we sequenced, assembled, annotated high-quality genome. results study will enrich , lay foundation for development promote evolutionary analysis Oleaceae species.

Language: Английский

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Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: April 25, 2024

Abstract Background Jasmine ( Jasminum ), renowned for its ornamental value and captivating fragrance, has given rise to numerous species accessions. However, limited knowledge exists regarding the evolutionary relationships among various species. Results In present study, we sequenced seven distinct species, resulting in assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that size 12 cp genomes ranged from 159 165 kb encoded 134–135 genes, including 86–88 protein-coding 38–40 tRNA 8 rRNA genes. J. nudiflorum exhibited a larger genome compared other mainly attributed elevated number forward repeats (FRs). Despite typically conservative nature chloroplasts, variations presence or absence acc D have been observed within sambac . The calculation nucleotide diversity Pi ) values 19 indicated potential mutation hotspots were more likely be located LSC regions than regions, particularly genes ycf 2, rbc L, atp E, ndh K, C > 0.2). Ka/Ks strong selection pressure on rps A, rpo C1, rpl 33 when comparing with three most closely related auriculatum , multiflorum dichotomum ). Additionally, SNP identification, along results Structure, PCA, phylogenetic tree analyses, divided into six groups. Notably, polyanthum showed gene flow signals both G5 group G3 tortuosum fluminense Phylogenetic analysis reflected same genus clustered together robust support Oleaceae, strongly supporting monophyletic Conclusion Overall, this study provides comprehensive insights genomic composition, variation, These enhance our understanding genetic history

Language: Английский

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Phylogenomics and Genetic Diversity of Arnebiae Radix and Its Allies (Arnebia, Boraginaceae) in China

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: June 9, 2022

Arnebiae Radix is a traditional medicine with pleiotropic properties that has been used for several 100 years. There are five species of Arnebia in China, and the two euchroma guttata source plants according to Chinese Pharmacopoeia. Molecular markers permit identification facilitate studies genetic diversity divergence wild populations these have not yet developed. Here, we sequenced chloroplast genomes 56 samples using genome skimming methods. The exhibited quadripartite structures lengths from 149,539 152,040 bp. Three variable ( rps16-trnQ , ndhF-rpl32 ycf1b ) were identified, more sites than universal markers. phylogenetic relationships among completely resolved whole sequences. arose during Oligocene diversified middle Miocene; this coincided geological events late early Miocene: warming progressive uplift Tianshan Himalayas. Our analyses revealed A. high levels comprise three subclades, respectively. clades significant differences diverged at 10.18 Ma Miocene. Pleistocene. results provided new insight into evolutionary history promoted conservation exploitation guttata.

Language: Английский

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OGRP: a comprehensive bioinformatics platform for the efficient empowerment of Oleaceae genomics research

Horticultural Plant Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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The Potential Risk Posed by Emerald Ash Borer to Cultivated and Wild Olive Trees

Forests, Journal Year: 2025, Volume and Issue: 16(2), P. 357 - 357

Published: Feb. 17, 2025

Emerald ash borer (EAB, Agrilus planipennis Fairmaire) is an Asian woodborer that a destructive pest of (Fraxinus spp.) trees throughout North America and in parts Asia Europe. It has killed hundreds millions worldwide the past two decades shown some ability to infest novel hosts, most notably white fringetree (Chionanthus virginicus L.). Here, I review evidence this beetle can succeed on cultivated olive (Olea europaea L), close relative fringetree. Studies observations thus far indicate that, while young are largely resistant EAB larval development, adults will oviposit trees, feed their foliage produce viable eggs, larger, older possibly stressed have potential support development adult stage field. soon interact with wild U.S. Europe, realized risk olives by be revealed.

Language: Английский

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The gap‐free genome assembly and multi‐omics analyses illustrate the evolutionary history and the synthesis of medicinal components of Ligustrum lucidum

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(4)

Published: Feb. 1, 2025

SUMMARY Ligustrum lucidum , an important ornamental and medicinal plant in the Oleaceae family, has become a globally notorious invasive species because of its high adaptability. However, lack quality genome hindered understanding genetic basis for broad adaptability mechanisms component synthesis. In this study, we successfully assembled gap free telomere to L. . Through reconstruction phylogenetic tree, presented evidence that Jasmineae diverged from earlier than Forsythieae, which challenges existing relationships within Oleaceae. Comparative genomics found two rounds gene family expansions significantly increased number genes related biotic abiotic stress resistances, may lay foundation Among fruits January March our investigation, results metabolome show be optimal harvesting time. By integrating genomic, transcriptomic, metabolomic data, identified candidate involved synthesis compounds, such as specnuezhenide, salidroside, oleanolic acid. This study provides valuable genomic resources comparative studies research

Language: Английский

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Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus)

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: April 15, 2025

Language: Английский

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A nearly complete genome assembly of multi-petal jasmine (Jasminum sambac) shed light into the flower variation and adaptability caused by chromosome variation from domestication

Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 229, P. 120892 - 120892

Published: April 21, 2025

Language: Английский

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Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 28, 2025

Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly ribosomal internal transcribed spacer, nrITS) plastid DNA sequences, resulting low-resolution phylogenetic trees uncertain intrageneric classifications. The genus, noted for its large genome, presents discordant relationships among Amana, Erythronium, Tulipa, likely due to incomplete lineage sorting (ILS) and/or reticulate evolution. Thus, phylogenomic approaches are needed clarify these the conflicting signals within tribe Tulipeae. We newly sequenced 50 transcriptomes 46 species Tulipeae (including multiple accessions all four genera) one outgroup sister Lilieae (Notholirion campanulatum), downloaded 15 previously published supplement sampling. One dataset (74 protein-coding genes, PCGs) (2594 orthologous OGs) were constructed, with latter used tree inference based maximum likelihood (ML) multi-species coalescent (MSC) methods. To investigate causes gene discordance, "site con/discordance factors" (sCF sDF1/sDF2) calculated first, after which nodes displaying high or imbalanced sDF1/2 selected network analyses polytomy tests determine whether ILS evolution best explain incongruence. Key not resolved by this technique, especially those further investigated applying D-statistics QuIBL. failed reconstruct reliable unambiguous evolutionary history pervasive evolution, caused either obscured minority signal differing genomic compartments. However, we confirmed monophyly most subgenera, exception two small subgenus Orithyia, heterophylla was recovered as remainder whereas T. sinkiangensis clustered Tulipa. In contrast, traditional sections found be non-monophyletic.

Language: Английский

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Original species identification of Epimedii Folium (Epimedium) and their distributional responses to climate change

Science of Traditional Chinese Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: May 2, 2025

Abstract Background Epimedii Folium is well known for its medicinal value. Four Epimedium species— Euphorbia brevicornu , E. sagittatum pubescens and koreanum —are the designated original plant s of Folium. Objective The objective this study to facilitate identification four species clarify their distributional responses climate change. Methods In study, we assessed genetic divergence identified molecular markers by using chloroplast genome sequences. Furthermore, forecasted distribution potentially suitable regions under Results authors obtained 26 sequences 1393 variable sites 273 indel events. Genetic analyses revealed that had long distance from other three species. Compared with complete genome, six hypervariable were discovered, both rps4-trnL ndhF chosen as Folium-specific DNA barcodes. Climate change expected influence geographical species, which primarily found in China, South Korea, Japan, leading expansion contraction ranges. Conclusions Two selected specific barcodes all addition, shift potential area various scenarios has been predicted. With support dynamics areas, are able establish a foundation sustainable utilization resources future.

Language: Английский

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