Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis DOI Creative Commons
Junqin Zong, Haoran Wang, Jingjing Wang

et al.

Research Square (Research Square), Journal Year: 2021, Volume and Issue: unknown

Published: Feb. 16, 2021

Abstract Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species individuals. However, as one of the most important warm-season turfgrasses widely used in USA China, cp characteristics position centipedegrass ( Eremochloa ophiuroides ) were poorly understood. Results: In this study, we determined complete chloroplast sequences E . using high-throughput Illumina sequencing technology. The circle pseudomolecule is 139,107 bp length, has a typical quadripartite structure consisting pair inverted repeat (IR) regions 22,230 each separated by large single copy (LSC) region 82,081 small (SSC) 12,566 bp. nucleotide composition asymmetric with an overall A + T content 61.60%. It encodes total 131 gene species, composed 20 duplicated genes within IR 111 unique including 77 protein-coding (PCGs), 30 transfer RNA (tRNA) four ribosome (rRNA) genes. Analysis repetitive revealed that contains 51 tandem repeats 29 forward, palindromic 2 reverse repeats, 197 simple (SSRs) which mainly adenine (A) thymine (T) bases. Comparison genomes other seven Gramineae showed high degree collinearity plants. Phylogenetic analysis was closely related to E. ciliaris eriopoda , placed clade two Mnesithea helferi subtribe Rottboelliinae, clarified evolutionary status tribe Andropogoneae also authenticated current Andropogoneae. Conclusions: present study provides genome, preliminarily ascertains Andropogonodae. This will be value grass taxa identification, resolution, population biodiversity, novel discovery functional genomic studies genus

Language: Английский

Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) DOI Creative Commons

Dongzhu Jiang,

Xiaodong Cai,

Min Gong

et al.

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

44
Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae DOI Creative Commons
Xinmiao Jia,

Jiaqi Wei,

Yuewen Chen

et al.

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

Published: Feb. 5, 2025

Language: Английский

Citations

1
The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus DOI Creative Commons

Chang‐Kun Liu,

Jia-Qing Lei,

Qiu‐Ping Jiang

et al.

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: March 7, 2022

Abstract Background The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although previous studies on provide us a good research basis, there are still unclear phylogenetic relationships taxonomic problems in , robust framework this has not been obtained, which severely hampers improvement revision system for genus. plastid genomes possessing more variable characters have potential reconstructing phylogeny Results In current study, we newly sequenced assembled seven genomes. Together five previously published performed comprehensively comparative analyses Twelve plastomes were similar terms genome structure, codon bias, RNA editing sites, SSRs, but varied size, gene content arrangement, border SC/IR. Fifteen mutation hotspot regions identified among that can serve as candidate DNA barcodes species identification . Our based generated high supports resolutions robustly supported non-monophyly Conclusion showed both conservation diversity. data efficient powerful improving complex summary, our study provides new sights into evolution, taxonomy, species.

Language: Английский

Citations

35
Physiological and transcriptome analyses in Yulania stellata under flooding stress DOI
Lin Xu, Lianlian Pan, Kang Ye

et al.

New Zealand Journal of Botany, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 24

Published: March 19, 2025

Language: Английский

Citations

0
Assembly and comparative analysis of the complete mitochondrial genome of <i>Yulania liliiflora</i>: an ornamental plant with high medicinal value DOI Creative Commons
Yunhan Chen, Wei Liu, Jing Qiu

et al.

Ornamental Plant Research, Journal Year: 2025, Volume and Issue: 5(1), P. 0 - 0

Published: Jan. 1, 2025

Language: Английский

Citations

0
High resolution melting of chloroplast mini-barcode in star anise (Illicium verum) authentication DOI

Qianru Zhou,

Bo Zhao, Jin Zhang

et al.

Industrial Crops and Products, Journal Year: 2023, Volume and Issue: 197, P. 116626 - 116626

Published: March 27, 2023

Language: Английский

Citations

8
Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants DOI Creative Commons
Junjun Yao,

Fangyu Zhao,

Yuanjiang Xu

et al.

BioMed Research International, Journal Year: 2020, Volume and Issue: 2020, P. 1 - 9

Published: Dec. 29, 2020

Dracocephalum tanguticum and moldavica are important herbs from Lamiaceae have great medicinal value. We used the Illumina sequencing technology to sequence complete chloroplast genome of D. then conducted de novo assembly. The two genomes a typical quadripartite structure, with gene’s lengths 82,221 bp 81,450 bp, large single-copy region’s (LSC) small (SSC) 17,363 17,066 inverted repeat (IR) 51,370 51,352 respectively. GC content was 37.80% 37.83%, plants encode 133 132 genes, respectively, among which there 88 87 protein-coding as well 37 tRNA genes 8 rRNA genes. Among them, rps2 gene is unique tanguticum, not found in moldavica. Through SSR analysis, we also 6 mutation hotspot regions, can be molecular markers for taxonomic studies. Phylogenetic analysis showed that more closely related Mentha.

Language: Английский

Citations

22
Morphological, physiological and biochemical changes in Magnolia zenii Cheng seed during development DOI Creative Commons
Shan Wang,

Yongbao Shen,

Huapeng Bao

et al.

Physiologia Plantarum, Journal Year: 2021, Volume and Issue: 172(4), P. 2129 - 2141

Published: May 3, 2021

Abstract An understanding of the seed dynamics endangered plant species, such as Magnolia zenii Cheng, is important for successful conservation. This study examined morphological, physiological and biochemical changes that occur in M. Cheng during development to determine appropriate harvest stage. The appearance seeds was influenced by occurring developmental period, which colour fruits changed from green red, while light brown dark brown. There a significant decrease moisture content 90 120 days after flowering (DAF); however, there no change 135 165 DAF. DAF onwards showed developed cotyledonary embryos. viability exceeded 95% onwards; germination percentage 0, hypothesising might exhibit dormancy under certain conditions this experiment. increase fat, soluble sugar starch approaching maturity. were malate dehydrogenase (MDH), glucose‐6‐phosphate (G‐6‐PDH), 6‐phosphogluconate (6‐PGDH) β‐amylase activities period. At 135–165 DAF, MDH activity remained stable, whereas 6‐PGDH reached its maximum, indicating underwent vigorous metabolism. findings provide theoretical basis researching time.

Language: Английский

Citations

11
Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species DOI Creative Commons
Huanhuan Xie, Lei Zhang, Cheng Zhang

et al.

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: Oct. 20, 2022

Abstract Background The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus contains eight species, but six of these species are threatened. No studies date characterized the characteristics chloroplast genomes (CPGs) within species. In this study, we compared structure CPGs, identified mutational hotspots resolved phylogenetic relationship . Results CPGs ranged in size from 160,027 bp 160,114 bp. A total 131 genes were identified, including 86 protein-coding genes, ribosomal RNA 37 transfer genes. We detected neither major expansions or contractions inverted repeat region, nor rearrangements insertions 300 large sequences (forward, reverse, palindrome repeats), 847 simple sequence repeats, five highly variable regions identified. One gene ( ycf1 ) four intergenic psbA-trnH-GUG , petA - psbJ rpl32-trnL-UAG, ccsA-ndhD) as by their nucleotide diversity Pi values (≥ 0.004), which useful for discrimination. Maximum likelihood Bayesian inference trees concordant indicated that Magnoliaceae consisted two genera Liriodendron Six clustered a monophyletic clade, forming sister clade with Yulania (BS = 100%, PP 1.00). Due non-monophyly should be treated section Within M. sinica diverged first (posterior probability 1, bootstrap 100), followed nitida, kachirachirai lotungensis omeiensis was yunnanensis 0.97, 50). Conclusion information provided our study could identification, conservation genetics resolving relationships

Language: Английский

Citations

8
Molecular Characterization and Phylogenetic Analysis of Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence DOI Creative Commons
Haoran Wang, Yuan Zhang, Ling Zhang

et al.

Current Issues in Molecular Biology, Journal Year: 2024, Volume and Issue: 46(2), P. 1635 - 1650

Published: Feb. 19, 2024

Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass well pasture in tropical and subtropical regions, with wide application land surface greening soil conservation South China southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for 139,107 bp length, quadripartite structure consisting large single copyregion 82,081 small copy region 12,566 separated by pair inverted repeat regions 22,230 each. overall A + T content whole 61.60%, showing asymmetric nucleotide composition. encodes total 131 gene species, composed 20 duplicated genes within IR 111 unique comprising 77 protein-coding genes, 30 transfer RNA 4 ribosome genes. sequence contains 51 long repeats 197 simple repeats, high degree collinearity among ophiuroide other Gramineae plants disclosed. Phylogenetic analysis showed ophiuroides, together two Eremochloa closely related to Mnesithea helferi subtribe Rottboelliinae. These findings will be beneficial classification identification taxa, phylogenetic resolution, novel discovery, functional genomic studies genus Eremochloa.

Language: Английский

Citations

1