Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution DOI Creative Commons
Rongrong Yan,

Yanfei Geng,

Yuhuan Jia

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Sept. 26, 2023

The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on few short DNA markers have made great contributions to taxonomy of limited sampling and low resolution tree failed resolve controversies between some generic circumscriptions. plastid genome exhibits powerful ability solve relationships ranging shallow deep taxonomic levels. To date, no phylogenomic been carried out in Linderniaceae.In this study, we newly sequenced 26 genomes including eight genera 25 species, explore evolution family through comparative genomic analyses.The size Linderniaceae ranged 152,386 bp 154,402 bp, exhibiting typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding 30 tRNA four rRNA genes. inverted repeat regions were more conserved compared with single-copy regions. A total 1803 microsatellites 1909 long sequence repeats identified, five hypervariable (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, ycf1) screened out. Most genes relatively conserved, only ycf2 gene found under positive selection species. Phylogenomic analyses confirmed that was distinctive lineage revealed presently circumscribed Vandellia Torenia non-monophyletic.Comparative showed highly conservative terms structure, order, content. Combining morphological molecular evidence, supported Yamazakia separating monotypic Picria as separate genus. These findings provide further evidence recognize among new insights into genomes.

Language: Английский

Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China DOI Creative Commons

Aerguli Jiamahate,

Tohir A. Bozorov, Jiancheng Wang

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(1), P. 99 - 99

Published: Jan. 1, 2025

The Tianshan wild fruit forest region is a vital repository of plant biodiversity, particularly rich in the unique genetic resources endemic medicinal plants this ecological niche. However, human activities such as unregulated mining and excessive grazing have led to significant reduction diversity these plants. This study represents first application DNA barcoding 101 found forests, using three loci along with morphological identification methods. A phylogenetic analysis was performed delineate species relationships. results indicate that internal transcribed spacer (ITS) has been identified most reliable barcode for across different families, while combining data from multiple gene segments can improve detection. Moreover, Analytical Hierarchy Process (AHP) employed assess prioritize plants, highlighting 23 candidates urgent conservation efforts region. approaches insights provide benchmark studies on local significance establish an evaluative framework biodiversity surveillance among area.

Language: Английский

Citations

1
Chloroplast Genome Evolution of Hamamelidaceae at Subfamily Level DOI Creative Commons
Yanlei Liu, Kangjia Liu, Wenpan Dong

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: March 27, 2025

ABSTRACT The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera 119 species. However, complete chloroplast genome sequences of species have been reported less frequently. In this study, five were newly sequenced, seven others available genomes added compare the evolution in at subfamily level. results indicated that size ranged from 158,116 159,941 bp, encoding 79 81 protein‐coding genes, four ribosomal RNA 30 31 transfer genes. A robust phylogenetic tree was obtained using genomes, supporting all formed a monophyletic group divided into subfamilies. Exbucklandioideae first diverged within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, Hamamelidoideae, which clade. Furthermore, three new potential DNA barcodes provided: trnH‐psbA , psbJ‐petA ycf1 . This study confirms data provide more accurate confident resolution relationships Hamamelidaceae. These genomic not only enhance understanding but also better

Language: Английский

Citations

1
Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae) DOI Open Access
Xinyu Liu,

Yuran Bai,

Yachao Wang

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16130 - 16130

Published: Nov. 9, 2023

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced whole chloroplast genome of H. and compared variation among five species to discover dynamic changes elucidate mechanisms that lead rearrangements in genomes. The 139,725 bp, exhibiting circular quadripartite structure with two copies inverted repeats (IRs) separating large single-copy region small region. encodes 106 unique genes, including 73 protein-coding 29 tRNAs, 4 rRNAs. genomes exhibit rearrangement significant variations species. size was remarkably associated expansion or contraction IR regions gene losses. Three genes-trnK-UUU, infA, rps16-were lost, three genes-rps7, rpl23, rpl32-were pseudogenized Hypericum. All lost introns clpP, intron rps12, second ycf3. contain many long repeat sequences, suggesting role facilitating rearrangements. Most according molecular evolution assessments, are under purifying selection.

Language: Английский

Citations

12
Comprehensive analysis of the effects of climate change on the species distribution and active components of Leonurus japonicus Houtt. DOI
Chao Chen, Lili Zhou, Ying Han

et al.

Industrial Crops and Products, Journal Year: 2024, Volume and Issue: 218, P. 119017 - 119017

Published: June 18, 2024

Language: Английский

Citations

4
Assembly and analysis of the complete mitochondrial genome of Leonurus japonicus (Lamiaceae) DOI Creative Commons
Qun Hu, Qing Li, Ying Mao

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 18, 2025

Language: Английский

Citations

0
Genetic diversity and phylogenetic analysis of Leonurus L. species under the conditions of Uzbekistan DOI Creative Commons
Nodira Arabova,

Gavharkhon Bahodirova,

G'appar Bobonazarov

et al.

BIO Web of Conferences, Journal Year: 2025, Volume and Issue: 173, P. 01006 - 01006

Published: Jan. 1, 2025

This study investigates the genetic diversity and evolutionary relationships within genus Leonurus , focusing on species found in Uzbekistan. For first time region, molecular tools were applied to analyze using Internal Transcribed Spacer (ITS) markers. Samples collected from Tashkent region sequenced, additional ITS data 21 representatives of Lamiaceae family retrieved GenBank. The sequences aligned CLUSTALW tool, refined with Snap Gene, analyzed Maximum Likelihood (ML) method Kimura 2-parameter (K2P) model IQ-TREE program. resulting phylogenetic tree revealed among closely related genera like Lagochilus Paraphlomis . High bootstrap values (99.9%–100%) confirmed reliability these findings. sp. UZB clustered glaucescens turkestanicus suggesting a shared origin. Close proximity was observed between cardiaca while sibiricus more genetically distant, likely due ecological or geographical isolation. Additionally, analysis highlighted significant differences indicating early divergence. These findings provide valuable insights into structure history species, emphasizing need preserve similar together for long-term population stability. research also underscores practical importance such studies biodiversity conservation adaptive management. Future work should expand genome-level analyses explore environmental factors influencing variation populations enhance efforts sustainable use plant resources.

Language: Английский

Citations

0
Original species identification of Epimedii Folium (Epimedium) and their distributional responses to climate change DOI Creative Commons
yiheng wang, Kangjia Liu, Meng Li

et al.

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

Citations

0
Comparative study on chloroplast genome of Tamarix species DOI Creative Commons
Yanlei Liu,

Kuo Ding,

Lixiong Liang

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(10)

Published: Oct. 1, 2024

Abstract Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total in this family. It is most widely distributed diverse genus They have important ecological significance transforming deserts improving climate conditions. However, poorly classified genera among flowering plants owing to its large variability high susceptibility interspecific hybridization. In study, complete chloroplast genomes three one draft genome were obtained study. Combined with eight deposited GenBank, sequences 12 used further analysis. There are 176 non‐SSR‐related indels 681 non‐indel‐related SSRs genomes. The mononucleotide prevalent all types SSRs. mVISTA results indicate sequence similarities across genome, suggesting that highly conserved, except sample androssowii (ENC850343). IR regions coding more conserved than single‐copy noncoding regions. trnF‐ndhJ , ndhC‐trnM‐ CAU, ycf1 trnL‐ UAG ‐ndhF variable higher those universal DNA markers. Finally, first phylogenetic tree was constructed which confirmed monophyly Tamaricaceae. based on date, changes branch length support rate can potentially help us clarify relationships . All genetic resources will facilitate future studies population genetics, identification, conservation biology

Language: Английский

Citations

3
Deciphering the evolutionary imprints of Camellia oleifera Abel.: delineating its distinct phylogeographic structure and demographic history through microsatellite and plastid fragment DOI Creative Commons
Tao Chen, T. Xiang, Zheng Qian

et al.

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

Published: April 25, 2025

Investigating the population structure and demographic history is crucial for elucidating evolutionary imprints of a species laying foundation effective utilization its germplasm. Camellia oleifera Abel., traditional woody oil-producing species, widely distributed in south Yangtze River China. However, phylogeography genetic diversity wild remain poorly understood. Data 20 simple sequence repeat (SSR) markers two chloroplast DNA (cpDNA) fragments was generated to assess variation differentiation across 33 natural populations. The integrated Approximate Bayesian Computation (ABC) ecological niche modeling (ENM) were utilized analyze history. analysis revealed high at level significant within populations both SSR cpDNA datasets. evidence based on indicated no noteworthy divergence phylogeographical structure. Haplotype phylogenetic analyses suggest that temporal pattern diversification likely associated with abrupt uplift Hengduan Mountains adjacent regions (HMR) during late Miocene Pliocene. In contrast, data discernible geographic pattern: divided into lineage regions, namely HMR Central-East identification potential refugia C. LGM, southeastern China, achieved through comprehensive combining ENM analysis. presence distinct patterns observed makers may account divergent hereditary characteristics between nuclear genomes, resulting disparate phylogeographic patterns. Nanling mountain range regarded as dispersal conduit facilitated gene flow refugia, leading extensive distribution stable trajectory oleifera. These methods findings can provide reference uncovering perennial oil crops facilitate resources breeding.

Language: Английский

Citations

0
Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data DOI Creative Commons
Jiahui Sun, Yiheng Wang,

Ping Qiao

et al.

Plants, Journal Year: 2023, Volume and Issue: 12(12), P. 2231 - 2231

Published: June 6, 2023

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana variation architecture phylogeny, we investigated the of 104 P. accessions from across China. montana's showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms 556 indels. The intergenic spacers, psbZ-trnS ccsA-ndhD, are two mutation hotspot regions in genome. Phylogenetic analysis based on dataset supported four clades. variations were among within clades, which gene flow levels. Most clades estimated to diverged at 3.82-5.17 million years ago. Moreover, East Asian summer monsoon South may accelerated divergence. Our results show that sequences highly variable can be used as molecular markers assess genetic relationships montana.

Language: Английский

Citations

7