Erwerbs-Obstbau, Journal Year: 2023, Volume and Issue: 65(5), P. 1315 - 1320
Published: March 7, 2023
Language: Английский
BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)
Published: Jan. 18, 2023
The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and Far East Asia. This contains about 100-150 species, with many species valued as important agricultural, medicinal horticultural resources. However, genomic resources suitable molecular markers for identification are currently sparse.We conducted comparative genomics phylogenetic analyses on species. chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist a large single copy (LSC, 86,986-88,200 bp), small (SSC, 15,498-15,891 pair inverted repeats (IRs, 29,765-29,934 bp). genomes contain 113 unique genes, including 79 protein coding 30 tRNA 4 rRNA genes. structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long conservative Zingiber. analysis divergence indicates following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 ycf3). Eight highly variable regions identified seven intergenic (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA ndhF-rpl32) one genic (ycf1). revealed sect. was sister to Cryptanthium rather than Pleuranthesis.This study reports 14 complete Overall, this provided solid backbone phylogeny polymorphisms we have uncovered sequencing offer rare possibility (for Zingiber) generation DNA markers. These results provide foundation future studies seek understand evolutionary dynamics or individual population variation
Language: Английский
Citations
45
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
Citations
37
BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)
Published: Jan. 5, 2024
Abstract Background The orchids of the subtribe Coelogyninae are among most morphologically diverse and economically important groups within subfamily Epidendroideae. Previous molecular studies have revealed that is an unambiguously monophyletic group. However, intergeneric infrageneric relationships largely unresolved. There has been long controversy over classification genera subtribe. Results complete chloroplast (cp.) genomes 15 species in were newly sequenced assembled. Together with nine available cp. GenBank from representative clades subtribe, we compared elucidated characteristics 24 genomes. results showed all shared highly conserved structure contained 135 genes arranged same order, including 89 protein-coding genes, 38 tRNAs, eight rRNAs. Nevertheless, structural variations relation to particular at IR/SC boundary regions identified. diversification pattern high consistency phylogenetic placement Coelogyninae. number different types SSRs repeats exhibited significant differences genomes, wherein mononucleotide (A/T), palindromic abundant. Four mutation hotspot ( ycf1a , ndhF-rp132 psaC-ndhE rp132-trnL ) determined, which could serve as effective markers. Selection pressure analysis three rpoC2 ycf2 genes) might experienced apparent positive selection during evolution. Using alignments whole sequences, this study presents a well-resolved framework Conclusion inclusion 55 plastid genome data nearly generic-level sampling provide comprehensive view illustrate genetic variation patterns species-rich plant inferred informally recognized major presented. markers identified here will facilitate future on genetics phylogeny
Language: Английский
Citations
9
BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)
Published: March 29, 2025
Juss. is a small herbaceous genus within the Bignoniaceae family. It comprises 16 species, which are subdivided into five subgenera. The species distributed mainly in Himalaya-Hengduan Mountains, although there exceptions, including I. sinensis, algae, semiretschenskia, and potaninii. Phylogenetic analyses based on trnL-F nr ITS sequences provided support for monophyly of its However, interspecific relationships among subgenera remain unresolved, further investigation necessary to elucidate these relationships. In this study, we sequenced assembled 34 chloroplast genomes from 12 Incarvillea representing all subgenera, explored phylogeny cp. genome data. results demonstrated that newly exhibited lengths between 159,132 169,244 bp, encoded total 129-141 genes. These included 84-95 protein-coding genes, 37 or 38 tRNA eight rRNA A comparative analysis revealed structural rearrangements expansions/contractions IR regions species. mutation hotspot were identified Incarvillea, encompassing six genes (atpI, psaI, rps18, trnQ-UUG, infA ycf1) intergenic spacer (psbT-psbf1, rps11-rpl36, infA-rps8, trnN-GUU-ycf1, ndhE-ndhG ndhI-ndhA). Pi values highly variable exceeded 0.06. phylogenetic corroborated elucidated subgenere, namely ((Niedzwedzkia, Incarvillea), ((Amphicome, Olgaea),Pteroscleris)). comprehensive comparison genomic diversity terms size, gene content order genomes. Based data, robust tree was generated through analysis, with well resolved. study enhance understanding evolutionary history genus, will facilitate studies resource protection genus.
Language: Английский
Citations
1
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
Citations
8
Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)
Published: Feb. 21, 2024
The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of species been limited. Using Illumina sequencing, we assembled annotated whole genomes seven (Gleditsia sinensis, japonica var. delavayi (G. delavayi), G. fera, japonica, microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), microphylla mutant). revealed that have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative analysis showed most (65.8-75.8%) abundant simple sequence repeats in Gymnocladus were located large single copy region. prefer T/A-ending codons avoid C/G-ending codons, positive selection was acting on rpoA, rpl20, atpB, ndhA ycf4 genes, genes underwent purifying selection. Expansion contraction inverted repeat (IR)/single (SC) region similar patterns within genus. Polymorphism coding regions more conserved than non-coding regions, IR SC Mutational hotspots mostly found intergenic such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", "rpl32-trnL" Gleditsia. Phylogenetic fera is closely related sinensis,G. are relatively related. Zhū Zào can be considered bud mutation sinensis. albino phenotype mutant not caused by variations genome, occurrence may due mutations chloroplast-related involved splicing or localization functions. This study will help us enhance our exploration genetic evolution geographical origins
Language: Английский
Citations
6
BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)
Published: Nov. 9, 2022
Species in genus Amomum always have important medicinal and economic values. Classification of using morphological characters has long been a challenge because they exhibit high similarity. The main goals this study were to mine genetic markers from cp genomes for species identification discover their evolutionary history through comparative analysis.Three villosum, maximum longipetiolatum sequenced annotated the complete chloroplast (cp) genomes, A. first reported. Three exhibited typical quadripartite structures with 163,269-163,591 bp length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs 3 rRNAs genes. 113-152 SSRs 99 repeats identified three genomes. By designing specific primers, we amplified highly variable loci mined marker ccsA relatively resolution Amomum. nonsynonymous synonymous substitution ratios (Ka/Ks) Alpinia showed that most subjected purifying selection. Phylogenetic analysis revealed relationships proved is paraphyletic. In addition, sample villosum was found be hybrid, becoming report natural hybridization genus. Meanwhile, high-throughput sequencing-based ITS2 an efficient tool interspecific hybrid help genome, parents can also determined.The conducive
Language: Английский
Citations
19
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: May 10, 2023
Small cardamom (Elettaria cardamomum Maton), the queen of spices, is third most expensive spice in world after saffron and vanilla, valued highly for its aroma taste. This perennial herbaceous plant a native coastal parts Southern India displays significant amount morphological diversity. Its genetic potential has not been exploited due to lack genomic resources limiting our understanding genome important metabolic pathways which give it economic advantage industry. Here, we report upon de novo assembled, draft whole sequence variety, Njallani Green Gold. We used hybrid assembly strategy using reads from Oxford Nanopore, Illumina 10x Genomics GemCode sequencing chemistries. The assembled length was 1.06 Gb (gigabases) close estimated size cardamom. More than 75% captured 8000 scaffolds with N50 0.15 Mb. appears have high repeat content 68055 gene models were predicted. Musa species an expansion contraction different families. silico mining simple repeats (SSRs). A total 2,50,571 SSRs identified 2,18,270 perfect 32,301 compound SSRs. Among SSRs, trinucleotides abundant (1,25,329) hexanucleotide appear least (2,380). From mined, 2,27,808 primer pairs designed based on flanking information. Wet lab validation performed 246 SSR loci their amplification profiles, 60 markers diversity analysis set diverse accessions. average number alleles detected per locus 14.57 minimum 4 maximum 30 alleles. Population structure revealed presence degree admixtures could primarily be cross-pollination prevalent this species. would help development or trait-linked can subsequently marker-assisted breeding crop improvement information utilization generation developed into public database, 'cardamomSSRdb' that freely available use by community.
Language: Английский
Citations
7
International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 15031 - 15031
Published: Oct. 9, 2023
Zingiberales includes eight families and more than 2600 species, with many species having important economic ecological value. However, the backbone phylogenetic relationships of still remain controversial, as demonstrated in previous studies, molecular dating based on chloroplast genomes has not been comprehensively studied for whole order. Herein, 22 complete from 21 were sequenced, assembled, analyzed. These displayed typical quadripartite structures, which ranged 161,303 bp to 163,979 length contained 111-112 different genes. The genome gene contents, simple sequence repeats, long codon usage highly conserved, slight differences among these genomes. Further comparative analysis 111 Zingiberales, including newly sequenced ones remaining national center biotechnology information (NCBI) database, identified three divergent regions comprising ccsA, psaC, psaC-ndhE. Maximum likelihood Bayesian inference analyses sequences found identical topological structures a strongly supported relationships. Cannaceae was sister Marantaceae, forming clade that collectively (Costaceae, Zingiberaceae) strong support (bootstrap (BS) = 100%, posterior probability (PP) 0.99-1.0); Heliconiaceae (Lowiaceae, Strelitziaceae), then Musaceae (BS 94-100%, PP 0.93-1.0); ((Cannaceae, Marantaceae), Zingiberaceae)) (Musaceae, (Heliconiaceae, Strelitziaceae))) robust 1.0). results divergence time estimation indicated crown node occurred approximately 85.0 Mya (95% highest density (HPD) 81.6-89.3 million years ago (Mya)), major family-level lineages becoming 46.8 80.5 Mya. findings proved could contribute study well provide potential markers further taxonomic studies Zingiberales.
Language: Английский
Citations
7
Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 839 - 839
Published: June 26, 2024
Cephaleuros species are well-known as plant pathogens that cause red rust or algae spot diseases in many economically cultivated plants grow shady and humid environments. Despite their prevalence, the adaptive evolution of these remains poorly understood. We sequenced characterized three (Cephaleuros lagerheimii, diffusus, virescens) chloroplast genomes, compared them with seven previously reported genomes. The sequences C. virescens were 480,613 bp, 383,846 472,444 bp length, respectively. These genomes encoded 94 genes, including 27 tRNA 3 rRNA 64 protein-coding genes. Comparative analysis uncovered variation genome size was principally due to length intergenic spacer sequences, followed by introns. Furthermore, several highly variable regions (trnY-GTA, trnL-TAG, petA, psbT, trnD-GTC, trnL-TAA, ccsA, petG, psaA, psaB, rps11, rps2, rps14) identified. Codon bias revealed codon usage pattern is predominantly shaped natural selection. Additionally, six genes (atpF, chlN, psbA, rbcL) determined be under positive selection, suggesting they may play a vital roles adaptation low-light intensity habitats.
Language: Английский
Citations
2