Comparative chloroplast genome analysis of Citrus (Rutaceae) species: Insights into genomic characterization, phylogenetic relationships, and discrimination of subgenera

Scientia Horticulturae, Journal Year: 2023, Volume and Issue: 313, P. 111909 - 111909

Published: Feb. 8, 2023

Language: Английский

---

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e14573 - e14573

Published: Feb. 3, 2023

The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most them being endemic to China. accurate identification endangered China is necessary for their conservation. Chloroplast genome sequences can play important role identification. In this study, comparative chloroplast analyses were conducted on diverse primarily distributed Despite the conserved nature genomes, we detected some highly divergent intergenic regions ( petA–psbE , ndhF–rpl32 psbM–trnD -GUC) as well three genes rbcL ycf1 ycf2 ) potential applications phylogenetics evolutionary analysis. phylogenetic analysis indicated various divided into clades. complete was better suited species. addition, based phylogeographical China, inferred first originated Yunnan then spread other southern areas Yangtze River. results research will add existing case studies contribute conservation danger extinction.

Language: Английский

---

Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships

Genes, Journal Year: 2022, Volume and Issue: 13(9), P. 1550 - 1550

Published: Aug. 28, 2022

Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species genus are widely used for wide range medicinal and industrial aspects. At present, most studies related to gene resources restricted morphological analyses features individual genomes, currently available select molecular markers insufficient. In this study, we assembled annotated complete chloroplast genomes nine species Litsea, carried out series comparative analyses, reconstructed phylogenetic relationships within genus. The genome length ranged from 152,051 152,747 bp total 128 genes were identified. High consistency patterns codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) insertions deletions (InDels) discovered across Variations presence pseudogene ycf1Ψ, resulting IR contraction expansion, reported. hyper-variable rpl16 was identified its exceptionally high Ka/Ks Pi values, implying that those frequent mutations occurred as result positive selection. Phylogenetic recovered based on full protein-coding genes. Overall, both sequences potential provided study enrich genomic Litsea. Valuable analysis also further research evolutionary patterns, markers, deeper

Language: Английский

---

Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome

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

Published: April 18, 2024

Abstract Background Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, also horticultural rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources evolutionary relationships among them, well differences between C. Cucurbita species, remain unclear. Results We investigated chloroplast (cp) genomes 160 individuals from 31 populations in Yunnan, major production area China. found that cp genome ~151 kb contains 128 genes, which 86 are protein coding 34 encode tRNA, eight rRNAs. identified 64 SSRs, mainly AT repeats. The was contain total 204 SNP 57 indels, 21 haplotypes were study individuals. reverse repeat (IR) region contained few compared with this six Sequence difference analysis demonstrated most variable regions concentrated single copy (SC) region. Moreover, sequences be more similar species than those non-coding regions. phylogenies reconstructed 61 representative Cucurbitaceae reflected currently accepted classification, sister however, interspecific Conclusions These results will valuable classification contribute our understanding within genus .

Language: Английский

---

The complete chloroplast genome sequences of nine melon varieties (Cucumis melo L.): lights into comparative analysis and phylogenetic relationships

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: July 9, 2024

Melon ( Cucumis melo L.) is one of the most extensively grown horticulture crops world. Based on morphological characters, melon was formerly divided into two subspecies, ssp. and C. agrestis . However, present methods are still inadequate to distinguish between them. The phylogenetic analysis based chloroplast genome sequences could provide essential evidence for classification varieties. We sequenced genomes nine different varieties by Illumina Hiseq performed bioinformatic analyses including repeat element analysis, comparison analysis. results showed that has a typical quadripartite structure conserved across analyzed sequences. Its length ranges 155, 558 156, 569 bp, with total GC content varying from 36.7% 37%. found 127–132 genes in genomes, 85–87 protein-coding regions, 34–37 tRNA 6-8 rRNA genes. molecular structure, gene order, content, codon usage, long repeats, simple sequence repeats (SSRs) were mostly among genomes. Phylogenetic clearly ssp This study not only provides valuable knowledge chloroplasts, but also offers theoretical basis technical support genetic breeding melons.

Language: Английский

---

Metabolomic Analysis of Different Parts of Black Wax Gourd (Cucurbita pepo)

Foods, Journal Year: 2025, Volume and Issue: 14(6), P. 1046 - 1046

Published: March 19, 2025

This study employed ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) combined with multivariate analysis to investigate tissue-specific metabolic profiles in the peel, pulp, and seeds of black wax gourd (Benincasa hispida). A total 1020 metabolites were identified, including 520 primary (e.g., amino acids, lipids, organic acids) 500 secondary phenolic flavonoids, alkaloids). Significant divergence was observed across tissues: 658, 674, 433 differential identified between peel seeds, pulp respectively. Unique such as methyl 5-glucosyloxy-2-hydroxybenzoate 3,5-di-O-caffeoylquinic acid exclusive while 4-O-(6′-O-glucosyl-imino)-4-hydroxybenzyl alcohol fertaric specific seeds. KEGG pathway enrichment revealed distinct priorities: flavonoids acids dominated phenylpropanoids nucleotides lipids The exhibited highest metabolite abundance (14.27%), whereas accumulated most (26.62%), essential like L-tryptophan functional linoleic acid. These findings underscore nutritional bioactive potential underutilized by-products (peel seeds), providing a biochemical foundation for valorizing tissues food, pharmaceutical, agricultural industries.

Language: Английский

---

The complete chloroplast genome of Lagenaria abyssinica (Hook.f.) C.Jeffrey: comparative and phylogenetic analysis

Genetic Resources and Crop Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Language: Английский

---

Comparative Genomic and Phylogenetic Analysis of Chloroplasts in Citrus paradisi Mac.cv. Cocktail

Genes, Journal Year: 2025, Volume and Issue: 16(5), P. 544 - 544

Published: April 30, 2025

Background: Citrus paradisi Mac. cv. Cocktail is globally valued for its abundant nutrients and bioactive compounds, particularly in tropical subtropical regions. A novel albino phenotype mutant of C. (designated WT) was identified Quzhou subsequently named mosaic (MT). To distinguish from conventional grapefruit cultivars to elucidate genomic differences between WT MT, this study conducted a comprehensive comparison their chloroplast genomes with those previously reported species. Methods: The complete MT were assembled through Illumina PE150 sequencing, enabling detailed comparative evolutionary studies. Results: results revealed that both exhibit conserved quadripartite structure. Each genome measures 160,186 base pairs length, uniform GC content 38.5%. Annotation 138 genes (91 protein-coding, 10 rRNA, 37 tRNA), 82 repeats, A/U-biased codons. Genome boundaries showed identical but divergent other Citrus. 52 protein-coding comparable selection pressures MT. Phylogenetically, are closely related distinguished all the traditional grapefruits. Conclusions: unrelated variations. Chloroplast genomics supports Cocktail’s differentiation This expands resources establishes theoretical framework future research on varieties.

Language: Английский

---

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Sept. 26, 2022

Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data scarce, the gene evolution interspecific relationship still unclear. In this study, we sequenced annotated chrysandra cp combined it with previously published genomes for other Chinese species. results showed that six varied in length between 156,452 bp (P. chrysandra) 157,066 speciosa), but all contained 132 genes, GC content 37.3%, highly similar genes distribution codon usage. A total eleven intergenic spacer regions were found having highest levels divergence, eight divergence hotspots identified as molecular markers Phylogeography genetic diversity studies Polyspora. Gene selection pressure suggested five subjected positive selection. Phylogenetic relationships among species based on complete supported strongly, indicating potential be used super barcodes further analysis phylogeny entire genus. will provide valuable information identification, breeding evolutionary genus

Language: Английский

---

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

PLoS ONE, Journal Year: 2022, Volume and Issue: 17(5), P. e0263545 - e0263545

Published: May 3, 2022

Macadamia is a true dicotyledonous plant that thrives in mild, humid, low wind environment. It cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects scientific research value. However, information on the genetic resources of spp. remains scanty.The mitochondria (mt) genomes three economically important species, integrifolia, M. ternifolia tetraphylla, were assembled through Illumina sequencing platform. The results showed each species 71 genes, including 42 protein-coding 26 tRNAs, 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, analysis genes migrating from chloroplast (cp) mt performed species. Phylogenetic based genome 35 other was conducted reveal evolution taxonomic status Macadamia. Furthermore, characteristics genome, size GC content, studied comparison with 36 final non-synonymous (Ka) synonymous (Ks) substitution most underwent negative selections, indicating their importance genome.The findings this study provide better understanding will inform future genus.

Language: Английский

---