Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae

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

Published: Feb. 5, 2025

Language: Английский

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

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Jan. 14, 2023

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

Language: Английский

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Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 17, 2024

Abstract Background Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in tropical regions South America, Africa, and Southeast Asia, which some have important ornamental, medicinal ecological values. Previous studies on phylogenetic taxonomic Costaceae by using nuclear internal transcribed spacer ( ITS ) chloroplast genome fragments data had low resolutions. Additionally, structures, variations molecular evolution complete genomes still remain unclear. Herein, a total 13 including 8 newly sequenced 5 from NCBI GenBank database, representing all three distribution this were comprehensively analyzed for comparative genomics relationships. Result The possessed typical quadripartite structures with lengths 166,360 to 168,966 bp, comprising large single copy (LSC, 90,802 − 92,189 bp), small (SSC, 18,363 20,124 bp) pair inverted repeats (IRs, 27,982 29,203 bp). These coded 111 113 different genes, 79 protein-coding 4 rRNA genes 28 30 tRNAs genes. gene orders, contents, amino acid frequencies codon usage within highly conservative, but several intron loss, long repeats, simple sequence (SSRs) expansion IR/SC boundaries also found among these genomes. Comparative identified five divergent ndhF, ycf1-D2 , ccsA-ndhD rps15-ycf1-D2 rpl16-exon2-rpl16-exon1 . Five combined DNA + ndhF could be used potential markers future analyses identification Costaceae. Positive selection was eight cemA, clpP ndhA petB psbD rps12 ycf1 Maximum likelihood Bayesian trees sequences consistently revealed identical tree topologies high supports between Three clades divided Asian clade, Costus clade American clade. Tapeinochilos sister Hellenia Parahellenia cluster strong support results dating showed that crown age about 30.5 Mya (95% HPD: 14.9 49.3 Mya), then started diverge into around 23.8 10.1 41.5 Mya). diverged at 10.7 3.5 25.1 Conclusion can resolve relationships provide new insights evolution. would useful inference

Language: Английский

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Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 29, 2024

Abstract The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack robust taxonomy based on phylogenetic relationships, classification within this family is perplexing, there also scarcity reports chloroplast genomes many falling under classification. In study, we conducted comprehensive analysis by sequencing characterizing complete six plants, namely Pteroxygonum denticulatum , Pleuropterus multiflorus ciliinervis Fallopia aubertii dentatoalata convolvulus . Our findings revealed these possess with typical quadripartite structure, averaging 162,931 bp in length. Comparative analysis, codon usage repetitive sequence demonstrated high level conservation plants. Furthermore, unveiled distinct clade occupied P. while ciliinrvis displayed closer relationship three belonging genus. Selective pressure maximum likelihood trees showed total 14 protein-coding genes exhibited positive selection, psbB ycf1 having highest number amino acid sites. Additionally, identified four molecular markers, petN-psbM psal-ycf4 ycf3-trnS-GGA trnL-UAG-ccsA which exhibit variability can be utilized for identification

Language: Английский

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The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 12, 2024

Abstract Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with practices, facilitating scientific validation ancient remedies. This integration enhances public understanding medicine’s efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs small shrubs, exhibiting simple petiolate sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering precise identification taxonomic elucidation species. To address this gap, we assembled complete chloroplast (CP) genome geobombycis conducted reannotation comparative analysis seven additional within genus. The findings demonstrate that CP genomes these exhibit quadripartite structures, lengths ranging from 14,523 to 150,599 bp. Overall, structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding 36 tRNA 8 rRNA genes. Additionally, 78 98 SSRs long repeat sequences were detected , notably, 6 highly variable regions identified as potential markers through sequence alignment. Phylogenetic based on Bayesian inference maximum likelihood methods strongly supported phylogenetic position genus a member Stachydeae tribe. comprehensive bioinformatics study lays groundwork for classification, plant identification, genetic engineering, evolutionary studies, breeding research concerning medicinal plants

Language: Английский

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Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema

Biochemical Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

Language: Английский

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Comparative and phylogenetic analysis of complete chloroplast genomes of Phrynium s. s. and Stachyphrynium (Marantaceae) in China, including a new species

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: May 1, 2025

Plants of the genera Phrynium and Stachyphrynium traditionally used as ethnomedicine or for wrapping sticky rice dumpling in tropical south subtropical Asia, have a long history ethnobotanical use. China represents northernmost distribution Marantaceae Asia. Due to notably similar leaf morphology between these genera, herbarium specimens are frequently misidentified, especially during vegetative stages. Their morphological uniformity unclear interspecific genetic relationships pose significant challenges taxonomic classification species identification. To date, systematic revisions phylogeny their indigenous remain lacking. In this study, we conducted comparative chloroplast genomes analyses seven two China. The exhibited conserved structure, gene content, order codon usage bias, but diverged size SC/IR boundaries. Four variable regions were identified potential molecular markers Phylogenetic using CDS nrDNA strongly support distinct monophyletic groups, with subdivided into clades. These findings advance our understanding provide critical insights identification, utilization, conservation medicinal plants. Finally, describe illustrate new pyramidale Y. Tong & Z. Lin.

Language: Английский

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Phylogenomics and plastome evolution of Indigofera (Fabaceae)

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

Published: June 6, 2023

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, soil water conservation. The taxonomically difficult due to high level of overlap morphological characters interspecies, fewer reliability states classification, extensive adaptive evolution. Previous characteristic-based taxonomy nuclear ITS-based phylogenies have contributed our understanding However, lack chloroplast genomic resources limits comprehensive phylogenetic relationships evolutionary processes Indigofera.Here, we newly assembled 18 genomes Indigofera. We performed a series analyses genome structure, nucleotide diversity, analysis, pairwise Ka/Ks ratios, positive selection analysis by combining with allied Papilionoideae.The exhibited highly conserved structures ranged size from 157,918 160,040 bp, containing 83 protein-coding genes, 37 tRNA eight rRNA genes. Thirteen variable regions were identified, which trnK-rbcL, ndhF-trnL, ycf1 considered as candidate DNA barcodes identification Phylogenetic using maximum likelihood (ML) Bayesian inference (BI) methods based on complete genes (PCGs) generated well-resolved phylogeny species. monophyly was strongly supported, four monophyletic lineages (i.e., Pantropical, East Asian, Tethyan, Palaeotropical clades) resolved within genus. ratios showed values lower than 1, 13 significant posterior probabilities codon sites identified branch-site model, associated photosynthesis. Positive accD suggested experienced evolution pressures imposed their herbivores pathogens. Our study provided insight into structural variation genomes, relationships, These results will facilitate future studies identification, interspecific intraspecific delimitation, evolution,

Language: Английский

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Comparative and Phylogenetic Analysis of Six New Complete Chloroplast Genomes of Rubus (Rosaceae)

Forests, Journal Year: 2024, Volume and Issue: 15(7), P. 1167 - 1167

Published: July 4, 2024

Rubus includes a group of important plants with medicinal and culinary significance, as well ornamental value. However, due to its status one the largest genera in Rosaceae family frequent occurrences apomixis, hybridization, polyploidy among species, morphological identification this genus is highly challenging. The plastid genome serves valuable tool for studying evolutionary relationships plants. Therefore, based on raw data whole genomes from six popular taxa, complete Cp were assembled, annotated, subjected comparative phylogenetic analyses. In research, newly reported, which all had representative quadripartite formation, similar GC content (37.06%–37.26%), their size ranged 155,493 bp 156,882 bp. They encode 111 unique genes, containing 79 PCGs, 28 tRNA, 4 rRNA. analysis gene structure different groups showed that sequence genes relatively conservative, there was no rearrangement. Most PCGs high frequency codon usage bias purifying selection states. A nucleotide variable revealed IR areas less variation than SC areas, greatest diversity SSC area. Eleven hypervariable identified, rpl32-trnL, rpl32, rps16-trnQ, trnT-trnL, trnQ-psbK, trnK-rps16, rps15-ycf1, could be used labels genetic taxa identification. trees 72 constructed ML BI methods. results strongly support theory monophyletic sampled species arranged into seven subgenera. Overall, study sheds new light phylogeny genus, providing insights future studies expanded family.

Language: Английский

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Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Feb. 20, 2023

Abstract Background Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with values. cephalantha a sister species to G. possessing similar morphology and wider distribution. To explore phylogeny of two reveal potential hybridization, we adopted next-generation sequencing technology acquire their complete chloroplast genomes sympatric allopatric distributions, as along Sanger produce nrDNA ITS sequences. Results The plastid were highly between . lengths ranged 146,795 147,001 bp in 146,856 147,016 All consisted 116 genes, including 78 protein-coding 30 tRNA four rRNA genes pseudogenes. total length sequence was 626 bp, six informative sites. Heterozygotes occurred intensively individuals Phylogenetic analysis performed based on genomes, coding sequences (CDS), hypervariable (HVR), ITS. Analysis all datasets showed that formed monophyly. well separated phylogenetic trees using ITS, except for hybrids, but mixed genomes. This study supports are closely related, independent species. However, hybridization confirmed occur frequently distribution owing lack stable reproductive barriers. Asymmetric introgression, backcrossing, may probably lead genetic swamping even extinction Conclusion recently diverged which might not have undergone post-zygotic isolation. Though genome shows obvious advantage exploring relationships some complicated genera, intrinsic revealed because matrilineal inheritance here; nuclear or regions hence crucial uncovering truth. As species, faces serious threats both natural human activities; therefore, balance conservation utilization extremely critical formulating strategies.

Language: Английский

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