Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill DOI Open Access

Kamil Szandar,

Jakub Sawicki, Łukasz Paukszto

et al.

Genes, Journal Year: 2022, Volume and Issue: 14(1), P. 67 - 67

Published: Dec. 25, 2022

Pulsatilla patens is a rare and endangered species in Europe its population resources have significantly decreased over the past decades. Previous genetic studies of this made it possible to estimate diversity European describe structure chloroplast mitochondrial genomes. The main aim these was characterize variability genomes more detail at intra-population inter-population levels. Our study presents new organelle genome reference sequences that allow design novel markers can be starting point for testing hypotheses, modern biogeography P. patens, adaptive responses changing environments. included sixteen individuals from five populations located Northeastern Poland. Comparative analysis 16 plastomes 5 enabled us identify 160 mutations, including 64 substitutions 96 InDels. most numerous detected SNPs Indels (75%) were accumulated three intergenic spacers: ndhD—ccsA, rps4—rps16, trnL(UAG)—ndhF. mitogenome dataset, which than twice as large plastome (331 kbp vs. 151 kbp), revealed eight times fewer (8 64) six InDels (16 96). Both identified same number haplotypes—11 out individuals, but both organellar slightly differ haplotype clustering. Despite much lower variation, mitogenomic data provide additional resolution detection enabling molecular identification unrecognizable based on dataset.

Language: Английский

Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae) DOI Creative Commons

Dongjuan Zhang,

Jing Ren,

Hui Jiang

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 4, 2023

Abstract Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported size and gene contents plastomes, with little information on comparative analysis plastid genomes genus. Additionally, there are still some whose chloroplast genome has not been reported. In study, complete plastomes six were sequenced assembled, among them, P. campanulatum was for first time. Comparative phylogenetic analyses then conducted published three related species. Results indicated that whole plastome length ranged from 154,564 bp ( multiflorum ) 156,028 stenophyllum having a quadripartite structure LSC SSC separated by two IR regions. A total 113 unique genes detected each revealed content GC these highly identical. No significant contraction or expansion observed boundaries all except sibiricum 1, which rps19 pseudogenized owing incomplete duplication. Abundant long dispersed repeats SSRs genome. There five remarkably variable regions 14 positively selected identified Heteropolygonatum. Phylogenetic results based strongly supported placement alternate leaves sect. Verticillata , group characterized whorled leaves. Moreover, verticillatum cyrtonema displayed paraphyletic. This study characters Heteropolygonatum maintained high degree similarity. Five found be potential specific DNA barcodes . suggested leaf arrangement suitable basis delimitation subgeneric groups definitions require further study.

Language: Английский

Citations

14
Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes DOI Open Access
Jinliao Chen, Fei Wang, Chengyuan Zhou

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(15), P. 12473 - 12473

Published: Aug. 5, 2023

Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are great value floriculture garden designing because their beautiful flower shapes colors. Although the morphological boundaries clearly defined, relationship between other closely related genera still ambiguous terms phylogeny. To better understand phylogenetic relationships, this study used next-generation sequencing technology to investigate phylogeny DNA barcoding taxonomic unit using genetic information from six plastid genomes. quadripartite-structure plastomes ranged 147,244 bp 148,391 included 120 genes. Among them, 74 were protein coding genes, 38 tRNA genes 8 rRNA while ndh pseudogenized or lost. Four non-coding mutational hotspots (rpl20–rpl33, psbM, petB, rpoB–trnCGCA, Pi > 0.06) identified. A total 71–77 SSRs 19–46 long repeats (>30 bp) recognized plastomes, which mostly located large single-copy region. Phylogenetic analysis indicated was monophylic sister Renanthera. Moreover, our results confirmed can be divided into three major clades. These findings provide assistance for identification investigation Aerides, as well contributes future research on phylogenomics Orchidaceae.

Language: Английский

Citations

12
Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group DOI Creative Commons

Qian‐Qian Zhong,

Zehuan Wang,

Jiaju Xu

et al.

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

Published: March 27, 2025

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species China, with 13 being endemic. The high diversity of this presents taxonomic challenges, particularly M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze chloroplast genomes focus on explore structural differences phylogenetic relationships among these closely related species. We analyzed 16 Melanoseris samples, including 12 new from group. genome sizes ranged 152,255 152,558 bp exhibited typical quadripartite structure, an average GC content 37.7%. Each encodes 132 genes, 87 protein-coding 37 tRNAs, 8 rRNAs. Repeat analysis identified 89 105 dispersed repeats, 24 28 tandem 35 39 SSRs, mononucleotide A/T repeats most common. Sequence alignment revealed that variable regions were mainly concentrated single-copy regions. Nucleotide 0 0.00485, highlighting 10 mutation hotspot Phylogenetic showed limited differentiation within research enhances our understanding genetic laying foundation for future studies.

Language: Английский

Citations

0
The complete chloroplast genome of Lagenaria abyssinica (Hook.f.) C.Jeffrey: comparative and phylogenetic analysis DOI
Haixia Xu,

Guorong Yu,

Xiang Dong

et al.

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

Published: April 2, 2025

Language: Английский

Citations

0
Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae) DOI Creative Commons
Tao Xiao,

Lie-Fen He,

Liangliang Yue

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 14, 2022

Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design landscape gardens. Two species of are categorized endangered critically China's Red List international trade these orchids is currently strictly monitored by the Convention on International Trade Endangered Species Wild Fauna Flora (CITES). This paper reports de novo assembled annotated plastome four Renanthera; R. citrina, coccinea, imschootiana, philippinensis. The length sequences ranged from 144,673 bp (R. imschootiana) 149,007 coccinea) with GC content 36.6-36.7%. plastomes showed typical quadripartite structure, including large single-copy (84,241-86,404 bp), small (11,468-12,167 pair inverted repeats (24,482-25,715 bp) regions. Of 120 genes detected, 74 were protein coding, 38 tRNA, eight rRNA genes. rather conserved, but nucleotide variations that could distinguish them apart noticeable-the total number tandem 62 (in citrina); while long 21 imschootiana philippinensis) 43 citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) identified. Phylogenetic analyses based CDS using maximum likelihood (ML) Bayesian inference (BI) revealed closely related Holcoglossum, Neofinetia, Pendulorchis, Vanda. relationship between was fully resolved; monophyletic clade formed coccinea recorded first diverge rest. genetic data obtained this study serve useful resource for identification well contribute future research phylogenomics Orchidaceae.

Language: Английский

Citations

13
Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae) DOI Creative Commons
Li Feng, Ying Liu, Junhui Wang

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: March 16, 2022

Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite whorled leaves. C. bungei, fargesii f. duclouxii and sources of traditional precious wood in China, known as "kings wood". Due to a lack phenotypic molecular studies insufficient sequence information, intraspecific morphological differences, common DNA barcodes partial fragments cannot clearly reveal phylogenetic relationships Catalpa. Therefore, we sequenced complete chloroplast genomes six taxa genus analyzed their basic structure evolutionary relationships. The genome shows typical tetrad total length ranging from 157,765 bp (C. fargesii) 158,355 ovata). large single-copy (LSC) region ranges 84,599 85,004 ovata), that small (SSC) 12,662 12,675 inverted repeat (IR) regions 30,252 30,338 GC content were 38.1%. In total, 113 unique genes detected, there 19 IR regions. included 79 protein-coding genes, 30 tRNA four rRNA genes. Five hypervariable (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA rps15) identified by analyzing nucleotide polymorphisms, which might be serve potential for species. Comparative analysis showed single polymorphisms (SNPs) simple repeats (SSRs) highly diverse Codon usage patterns similar among present study. addition stop codons, all codons preference ending A T. Phylogenetic entire formed monophyletic group, reflecting genus. This study provides information on sequence, structural variation, codon bias phylogeny Catalpa, will facilitate future research efforts.

Language: Английский

Citations

8
Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental Pennisetum Rich. (Poaceae) DOI Creative Commons
Yidi Guo, Lingyun Liu, Yuesen Yue

et al.

Agronomy, Journal Year: 2022, Volume and Issue: 12(7), P. 1683 - 1683

Published: July 15, 2022

Pennisetum species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote preservation utilization of ornamental resources, we developed simple sequence repeat (SSR) markers from setaceum cv. ‘Rubrum’ transcriptome verified their conservation 38 sources. Our sequencing efforts generated 58.91 Gb clean data containing 55,627 unigenes. We functionally annotated 30,930 unigenes, with functions enriched translation ribosomal structure biogenesis. Database comparisons indicated that closest relative P. is Setaria italica. Over five thousand SSR were detected transcriptomic data. selected pairs highly polymorphic 50 randomly markers. Based on genetic diversity analysis sources, obtained 312 bands, an average 8.21 alleles per primer. Principal coordinate analyses generation a, which proved has moderate diversity. In addition, fingerprint maps constructed to improve identification. The by our study enhances transcriptional information available for setaceum. This lays foundation collection resources provides a basis future breeding projects using this species.

Language: Английский

Citations

8
Characterization of the complete chloroplast genome of purple flowering stalk (Brassica campestris var. purpuraria) and comparisons with related species DOI
Yihui Gong,

Limeng Duan,

Guihua Zhou

et al.

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: May 9, 2024

Language: Английский

Citations

1
Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet DOI
Chandan Kapoor,

Anamika,

S. Mukesh Sankar

et al.

Planta, Journal Year: 2024, Volume and Issue: 259(6)

Published: May 15, 2024

Language: Английский

Citations

1
Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution DOI Creative Commons
Jiao Fang, Benwen Liu, Guoxiang Liu

et al.

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: Dec. 8, 2021

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and spot diseases in vascular plants. No chloroplast genomes have yet been reported this genus, the limited genetic information obstacle to understanding evolution genus. In study, we sequenced six new Trentepohliales genomes, including four two Trentepohlia. The large compared most green algae, ranging from 216 408 kbp. They encode between 93 98 genes a GC content 26-36%. All were circular-mapping lacked quadripartite structure, contrast previously Trentepohlia odorata, does inverted repeat. duplicated trnD -GTC, petD, atpA C. karstenii may be remnants IR region shed light on its reduction. Chloroplast show elevated rates evolution, strong rearrangement dynamics several display alternative code reassignment UGA/UAG codon presumably coding arginine. Our results present first whole genome genus enrich resources Trentepohliales.

Language: Английский

Citations

8