Reporting Complete Chloroplast Genome of Endangered Red Mulberry Useful for Understanding Hybridization and Phylogenetic Relationships

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Фев. 12, 2025

Introgressive hybridization of the North American native red mulberry (Morus rubra) with its invasive congener white alba) has severely threatened genetic integrity M. rubra, which is primarily found in pristine riparian forests. The major objectives present study were 1) to sequence, assemble, and annotate complete chloroplast (cp) genome 2) perform phylogenomic analyses Morus species assess their evolutionary history events within genus. We sampled 45 trees representing populations from eight US states for cp sequencing. that rubra ranged 159,396 159,423 bp contained 128 genes coding rRNAs, 37 tRNAs, 83 proteins. was at least 103 larger than alba. cpDNA sequence polymorphism analysis showed presence 12 haplotypes. across Morus species identified trnK-UUU-rps16, psbI-trnG-UCC, psbC-psbZ, psbZ-trnM-CAU, rps4-trnT-UGU, trnT-UGU-trnL-UAA, ndhC-trnV-UAC, psbE-petL, clpP1, ndhF-rpl32, rpl32-trnL-UAG, ccsA-ndhDas having higher DNA (Pi > 0.01), making them candidate species-specific markers. Phylogenomic revealed distinct clades Asian, American, South African Morus, supporting monophyly Divergence time most common ancestor genus diverged 38.67 million years ago (MYA), separating clade M. mesozygia and insignis others, while Asian diverged 28.63 MYA. results this provide insights into structure rubra, offering foundational data addressing complex taxonomic complexities developing molecular markers population genetics, including introgressive hybridization.

Язык: Английский

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Phenotypic and RNA-seq Profiles Identified Key Pathways and Genes Involved in Gleditsioside Biosynthesis in Gleditsia sinensis Lam.

Forests, Год журнала: 2025, Номер 16(3), С. 393 - 393

Опубликована: Фев. 22, 2025

Gleditsia sinensis Lam. (G. sinensis) is a widely known medicinal plant, and its primary bioactive compound gleditsioside. So far, the significant economic value of gleditsioside has been recognized. However, transcriptional regulation governing biosynthesis during G. pod development remains unclear. In this investigation, we observed that levels increased in pods from June to November, performed transcriptome analysis explore phenomenon. A total 703 162 differentially expressed unigenes (DEGs) were identified terpenoid backbone triterpenoid pathways, respectively. total, 99 encoding 17 enzymes, such as ENIN, cytochrome P450 (CYP93E1), UDP-glucosyltransferase, pathway. Moreover, DEGs crucial HMGCR AGBH, might determine synthesis development. Interestingly, pathway extended ten metabolic including sterol brassinolide pathway, among other pathways involved various hormonal regulations. These shared same precursor substances (IPP DMAPP). addition, weighted gene correlation network (WGCNA) revealed CL5845.Contig1 (HMGCR) CL8823.Contig2 (LUP4) be biosynthesis. Furthermore, transient transformation validation experiments demonstrated overexpression (HMGCR), (LUP4), CL11248.Contig4 (CYP93E1) significantly enhanced Overall, our findings provide important genetic resources for future functional research new insights into basic mechanism saponin

Язык: Английский

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Reporting complete chloroplast genome of endangered red mulberry, useful for understanding hybridization and phylogenetic relationships

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Апрель 18, 2025

Introgressive hybridization of the North American native red mulberry (Morus rubra) with its invasive congener white alba) has severely threatened genetic integrity M. rubra, which is primarily found in pristine riparian forests. The major objectives present study were (1) to sequence, assemble, and annotate complete chloroplast genome (2) perform phylogenomic analyses Morus species assess their evolutionary history events within genus. We sampled 45 trees representing populations from eight US states for sequencing. that rubra ranged 159,396 159,423 basepair (bp) contained 128 genes coding rRNAs, 37 tRNAs, 83 proteins. was at least 103 bp larger than alba. DNA sequence polymorphism analysis showed presence 12 haplotypes. across identified trnK-UUU-rps16, psbI-trnG-UCC, psbC-psbZ, psbZ-trnM-CAU, rps4-trnT-UGU, trnT-UGU-trnL-UAA, ndhC-trnV-UAC, psbE-petL, clpP1, ndhF-rpl32, rpl32-trnL-UAG, ccsA-ndhD as having higher (Pi > 0.01). Phylogenomic revealed distinct clades Asian, American, South African Morus, supporting monophyly Divergence time most recent common ancestor genus diverged 38.67 million years ago (MYA), separating clade mesozygia insignis others, while Asian 28.63 MYA. results this provide insights into structure offering a foundational data bridges knowledge gaps addressing complex taxonomic complexities developing molecular markers population genetics, including introgressive hybridization.

Язык: Английский

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Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus Tulipa L.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Ноя. 12, 2024

Species of Tulipa are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features complete chloroplast genome sequence four local endangered species including T. alberti, kaufmanniana, greigii , dubia from Kazakhstan using Illumina sequencing technology. comparative analyses revealed that genomes were highly conserved terms total size (152. 006 bp - 152. 382 bp), a pair inverted repeat regions (26. 330 26. 371 separated by large single copy region (82.169 82,378 bp) small (17.172 -17.260 bp). Total GC content (36.58-36.62 %), gene number (131), intron length (540 2620 28 genes. showed nucleotide diversity (π =0,003257). SSR loci was 159 alberti 158 kaufmanniana 174 163 . result indicated ten CDS genes, namely rpoC2, cemA, rbcL, rpl36, psbH, rps3, rpl22, ndhF, ycf1 matK with effective polymorphic simple repeats (SSRs), high variability (SV) ranging 2.581 to 6.102, (Pi) these 0,004 0,010. For all intergenic longer than 150 bp, twenty one most variable found 4,848 11,862 0,01599 0,01839. Relative synonymous codon usage (RSCU) analysis identify overrepresented underrepresented codons each amino acid. Based phylogenic analysis, sequences clustered into major groups, reflecting distinct evolutionary lineages corresponding subgenera Eriostemons, Orithyia Notably, distinctively grouped Eriostemons rather other species, suggesting unique history potentially shaped geographical isolation or specific ecological pressures. provides fundamental information future research studies, even designing available molecular markers.

Язык: Английский

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Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Дек. 21, 2024

Although many complete chloroplast (cp) genomes of different types peppers have already been published, there has no comprehensive study that summarizes all the characteristics Peruvian landrace “arnaucho” chili pepper (ACP) comparing it with other in its Capsiceae tribe. In this study, a analysis was conducted using data from cp obtained NCBI GenBank. These 14 were annotated Geseq, followed by genomic comparisons, structure analysis, phylogeny, and repetitive sequence employing variety bioinformatics tools. The findings revealed length variations among genomes, ranging 156,583 bp C. lycianthoides to 157,390 pubescens, GC content 37% across genomes. comparative genome greatest variation occurred non-coding regions. Arnaucho exhibited greater divergence coding regions lycianthoides, specifically genes accD, rpl20, rps12, clpP, ycf2, ndhF, ndhA, ycf1, rpl2. results phylogeny pairwise distance support arnaucho clusters galapagoense, an average value 0.00002733. Additionally, determined ACP maintains number sequences similar Capsicum species but possesses lower SSRs (33). Finally, junction total 156,931 bp, galapagoense 156,959 bp. four boundary consistent gene patterns, except for JSB region, where ycf1 located only IRb whereas absent Capsicum species. This research provides additional effective evidence characterizing entire classifying species genera within

Язык: Английский

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