Comparative analysis of the complete chloroplast genomes of critically endangered legumes (Dalbergia, Papilionoideae): insights into genome structure, phylogeny, and conservation implications

Plant Systematics and Evolution, Journal Year: 2025, Volume and Issue: 311(2)

Published: March 27, 2025

Language: Английский

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Identification of AP2/ERF Transcription Factors and Characterization of AP2/ERF Genes Related to Low-Temperature Stress Response and Fruit Development in Luffa

Agronomy, Journal Year: 2024, Volume and Issue: 14(11), P. 2509 - 2509

Published: Oct. 25, 2024

Plant-specific APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factors are involved in the regulation of genes associated with growth and developmental processes numerous plants. Although AP2/ERF proteins from other species have been intensively studied, no studies reported on family Luffa cylindrica, an important vegetable cucurbit family, one most popular vegetables world. In this study, 133 (315–6696 bp) encoding LcAP2/ERF complete domains were identified according to luffa P93075 genome. These subsequently classified analyzed for their gene structures, chromosomal distribution locations, promoter cis-acting elements, conserved structural encoded proteins, responses abiotic stresses. The divided into five phylogenetic groups (AP2, DREBs, ERFs, RAV, soloists). unevenly distributed across 13 chromosomes. An analysis structures indicated contained 0–11 introns (average 4.4). Additionally, 16 motifs that different groups. Moreover, 11 elements response environment a 2000 bp region upstream promoters. A transcriptome involving RNA-seq data revealed tissue-specific expression profiles diversity expression. effects low-temperature stress determined. Furthermore, fruit-development-related low-temperature-induced expressional changes verified by RT-qPCR analyses 14 differentially expressed luffa. Our findings will help clarify evolution while also providing valuable insights future functions.

Language: Английский

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Deciphering the Plastomic Code of Chinese Hog-Peanut (Amphicarpaea edgeworthii Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe

Genes, Journal Year: 2024, Volume and Issue: 15(1), P. 88 - 88

Published: Jan. 11, 2024

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on Glycininae subtribe, by conducting comprehensive analysis of highly conserved plastome in Amphicarpaea edgeworthii Benth., critical species this subtribe. Through meticulous genomic sequencing, we identified size 148,650 bp, composed 128 genes, including 84 protein-coding 36 tRNA 8 rRNA genes. Comparative across seven illuminated universally circular quadripartite structure, nine genes exhibiting notable nucleotide diversity, signifying remarkable variability. Phylogenetic reconstruction 35 underscores affinity Glycine, placing Apios as sister lineage all other species, excluding Clitorinae Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, Spatholobus, traditionally clumped together Erythrininae display paraphyletic divergence, thereby contesting their coherence. pronounced structural differences boundary among taxa unresolved subtribal affiliations demand reevaluation Erythrininae’s classification, potentially refining contours tribe.

Language: Английский

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Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales

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

Published: Sept. 12, 2024

Language: Английский

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New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(23), P. 16629 - 16629

Published: Nov. 22, 2023

Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists 95 perennial and 35 annual species. Due lack stable diagnostic morphological characteristics high-resolution molecular markers, phylogenetic relationships Hydrocotyle need be further investigated. In this study, we newly sequenced assembled 13 whole plastid genomes performed comparative genomic analyses with four previously published plastomes phylogenomic within Araliaceae. The exhibited typical quadripartite structures lengths from 152,659 bp 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), small (SSC) (18,585-18,768 pair inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding 30 tRNA rRNA genes. Comparative showed that IR boundaries were highly similar, coding regions more conserved than non-coding (SC) regions. A total 2932 simple sequence 520 long identified, specificity in number distribution repeat sequences. Six hypervariable screened SC region, including intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, ndhF-rpl32) two genes (rpl16 ycf1). Three (atpE, rpl16, ycf2) subjected positive selection only few species, implying most relatively during evolutionary process. Plastid supported treatment Apiaceae topologies high resolution indicated data can used comprehensive research Hydrocotyle. currently may not accurately reflect genus, new taxonomic evaluated selected combination results.

Language: Английский

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Unraveling the phylogenetic position of a Korean endemic species Indigofera koreana (Fabaceae) through plastid genome analysis

Journal of Asia-Pacific Biodiversity, Journal Year: 2024, Volume and Issue: 17(3), P. 505 - 512

Published: May 17, 2024

Indigofera koreana is an endemic species to Korea, yet its phylogenetic position remains unresolved. In this study, we sequenced and analyzed plastid genomes (plastomes) clarify the standing of I. koreana. We produced next-generation sequencing data for close relative, kirilowii. The plastomes both were successfully assembled, measuring 159,517 bp kirilowii 159,459 Both shared same number 128 intact genes had identical 35.7% GC content. Phylogenetic analyses utilizing complete plastome coding sequence-only data, along with 20 other plastomes, conducted elucidate their evolutionary relationships. Our findings indicate that forms a monophyletic group decora, carlesii, kirilowii, supported by maximum bootstrap values. Specifically, tree derived from strongly suggests most closely related While these results are in line previously suggested infra-generic classifications, they highlight need more comprehensive genomic studies further unravel dynamics within genus, especially considering role polyploidization diversification.

Language: Английский

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Chloroplast genome sequencing in winged bean (Psophocarpus tetragonolobus L.) and comparative analysis with other legumes

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: July 19, 2024

The winged bean (Psophocarpus tetragonolobus) is a fast-growing, underutilized legume thriving in hot, humid regions. It forms symbiotic associations with broad-spectrum cowpea rhizobial group, making it ideal for crop rotation or intercropping systems. Winged seeds are rich protein, fiber, vitamins, minerals, fat, and carbohydrates, highlighting its potential as valuable agricultural crop. In this study, we conducted whole-genome sequencing of the chloroplast using high-coverage short-read on Illumina platform, generating over 1 billion paired-end raw reads. We utilized GetOrganelle toolkit to assemble genome comprising 130 genes, including 85 protein-coding 37 tRNAs, eight rRNA genes. also identified 84 perfect SSRs, two compound 15 VNTRs. Our analysis revealed typical quadripartite structure genome, along insights into functional classification phylogenetic relationships other legumes. Additionally, possible genomic rearrangements through synteny analysis. Characterizing provides crucial resources research improvement. Comparative genomics offers significant evolutionary molecular biology

Language: Английский

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