Green giant—a tiny chloroplast genome with mighty power to produce high‐value proteins: history and phylogeny

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(3), P. 430 - 447

Published: Jan. 23, 2021

Summary Free‐living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence chloroplast DNA was demonstrated in 1960s. The first genomes sequenced 1980s, followed ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop past three decades. Foreign genes expressed isolated chloroplasts or intact plant late 1980s stably integrated into genomes, with typically maternal inheritance shown 1990s. Since then, conferred highest reported levels tolerance resistance biotic abiotic stress. Although launching products agronomic traits important crops using this concept has been elusive, commercial developed include enzymes used everyday life from processing fruit juice, enhancing water absorption cotton fibre removal stains as laundry detergents dye textile industry. Plastid genome sequences have revealed framework green phylogeny well intricate history plastid transfer events other eukaryotes. Discordant historical signals among suggest possible variable constraints across plastome further understanding mitigation these may yield new opportunities for bioengineering. In review, we trace evolutionary chloroplasts, status autonomy recent advances use those advanced clinic, including treatment COVID‐19 patients SARS‐CoV‐2 vaccine.

Language: Английский

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Function of Chloroplasts in Plant Stress Responses

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(24), P. 13464 - 13464

Published: Dec. 15, 2021

The chloroplast has a central position in oxygenic photosynthesis and primary metabolism. In addition to these functions, the recently emerged as pivotal regulator of plant responses abiotic biotic stress conditions. Chloroplasts have their own independent genomes gene-expression machinery synthesize phytohormones diverse range secondary metabolites, significant portion which contribute response adverse Furthermore, chloroplasts communicate with nucleus through retrograde signaling, for instance, reactive oxygen signaling. All above facilitate chloroplast's exquisite flexibility responding environmental stresses. this review, we summarize recent findings on involvement regulatory various stresses including heat, chilling, salinity, drought, high light conditions, pathogen invasions. This review will enrich better understanding interactions between stresses, lay foundation genetically enhancing plant-stress acclimatization.

Language: Английский

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The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

International Journal of Molecular Sciences, Journal Year: 2020, Volume and Issue: 21(17), P. 6082 - 6082

Published: Aug. 24, 2020

Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes gene-expression machinery. Most genes from prokaryotic ancestors of were transferred into nucleus over course evolution. However, importance chloroplast gene expression environmental stress responses recently become more apparent. Here, we discuss emerging roles distinct processes to stresses. For example, transcription translation psbA play an important role high-light responses. A better understanding connection between is crucial for breeding stress-tolerant crops able cope with rapidly changing

Language: Английский

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Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships

BMC Plant Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Nov. 13, 2020

Abstract Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one most taxonomically difficult taxa within Apiaceae, largely due to varied morphological characteristics. To investigate plastome evolution and phylogenetic relationships , we determined complete sequences eight using a de novo assembly approach. Results Through comprehensive comparative analysis, found that plastomes were similar terms repeat sequence, SSR, codon usage, RNA editing site. However, compared with other seven species, L. delavayi exhibited striking differences genome size, gene number, IR/SC borders, sequence identity. Most genes remained under purifying selection, whereas four showed relaxed namely ccsA rpoA ycf1 ycf2 . Non-monophyly was inferred from internal transcribed spacer (ITS) analyses. Conclusion tree ITS produced incongruent topologies, which may be attributed hybridization incomplete lineage sorting. Our study highlighted advantage mass informative sites resolving relationships. Moreover, combined previous studies, considered current taxonomy system needs improved revised. In summary, our provides new insights into evolution, phylogeny, species.

Language: Английский

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Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

BMC Plant Biology, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 23, 2021

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in each possess 50 or more species, including Globba (100), Hedychium ( > 80), Kaempferia (50) Zingiber (150). Despite agricultural, medicinal horticultural importance these genomic resources suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled analyzed ten complete chloroplast genomes from nine species Zingiberoideae: lancangensis , marantina multiflora schomburgkii var. angustata coccineum neocarneum rotunda ‘Red Leaf’, ‘Silver Diamonds’ recurvatum . These (size range 162,630–163,968 bp) typical quadripartite structures that consist single copy (LSC, 87,172–88,632 bp), small (SSC, 15,393–15,917 pair inverted repeats (IRs, 29,673–29,833 bp). The contain 111–113 different genes, 79 protein coding 28–30 tRNAs 4 rRNA genes. dynamics genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long exhibit similarities, with slight differences observed among genomes. Further comparative analysis seventeen related 12 divergent hotspots identified. Positive selection 14 accD ccsA ndhA ndhB psbJ rbcL rpl20 rpoC1 rpoC2 rps12 rps18 ycf1 ycf2 ycf4. Phylogenetic analyses, based on chloroplast-derived single-nucleotide polymorphism data, strongly support Curcuma I + “ clade” consisting II, form nested evolutionary relationship Zingiberoideae. Conclusions Our study provides detailed information genomes, representing valuable resource future studies seek to understand identified can be used development phylogenetic inference identification closely within four

Language: Английский

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Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications

Genes, Journal Year: 2022, Volume and Issue: 13(3), P. 461 - 461

Published: March 4, 2022

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly annotation of complete chloroplast genome wax gourd 156,758 bp in total. The quadripartite structure comprises a large single-copy (LSC) region 86,538 small (SSC) 18,060 bp, separated by pair inverted repeats (IRa IRb) 26,080 each. Comparison analyses among B. three other species from Benincaseae presented significant conversion regarding nucleotide content, structure, codon usage, synonymous non-synonymous substitutions, putative RNA editing sites, microsatellites, oligonucleotide repeats. LSC SSC regions were found to be much more varied than IR through divergent analysis within Benincaseae. Notable contractions expansions observed, suggesting difference size, gene duplication deletion, presence pseudogenes. Intronic sequences, such as trnR-UCU-atpA atpH-atpI, observed highly regions. Two types phylogenetic based on cp 72 genes suggested sister relationships between Citrullus, Lagenaria, Cucumis. Variations consistency previous studies are discussed. provides valuable genetic information for detection molecular markers, research taxonomic discrepancies, inference Cucurbitaceae.

Language: Английский

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Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(8), P. 2207 - 2222

Published: Feb. 16, 2022

The last decade has witnessed huge technological advances in genomics, particularly DNA sequencing. Here, we review the actual and potential application of genomics supporting situ conservation crop wild relatives (CWRs). In addition to helping prioritization protection CWR taxa sites, genome analysis is allowing identification novel alleles that need be prioritized for conservation. Genomics enabling sources important adaptive traits can guide establishment or enrichment genetic reserves. Genomic tools also have developing a robust framework monitoring reporting genome-based indicators diversity changes associated with factors such as land use climate change. These been demonstrated an role managing populations, sustainable access utilization diversity, enhancing accelerated domestication new crops forensic thus preventing misappropriation resources. Despite this great potential, many policy makers managers failed recognize appreciate accelerate support management biodiversity CWRs underpin global food security. Funding inadequate genomic expertise among practitioners remain major hindrances widespread

Language: Английский

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Conservation and Global Distribution of Onion (Allium cepa L.) Germplasm for Agricultural Sustainability

Plants, Journal Year: 2023, Volume and Issue: 12(18), P. 3294 - 3294

Published: Sept. 18, 2023

Onion (Allium cepa L.) is recognized globally as a crucial vegetable crop, prized not only for its culinary applications but also numerous health-promoting properties. With climate change relentlessly exerting mounting challenges to agriculture, the preservation and deployment of onion germplasm has become critical ensuring sustainable agriculture safeguarding food security. Global collections function repositories genetic diversity, holding within them an extensive array valuable traits or genes. These can be harnessed develop varieties resilient adversities. Therefore, detailed information concerning from various geographical regions bolster their utility. Furthermore, amplified understanding importance fostering international inter-institutional collaborations becomes essential. Sharing making use resources provide viable solutions looming agricultural future. In this review, we have discussed worldwide distribution germplasm, along with implications sustainability. We underscored interinstitutional collaboration in collecting conservation

Language: Английский

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Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes

BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)

Published: March 18, 2021

Abstract Background Lima bean ( Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source plant proteins for human diet. As we all know, lima beans have economic value great diversity. However, our knowledge chloroplast genome level limited. Results The was obtained by Illumina sequencing technology first time. Cp with length 150,902 bp, including pair inverted repeats (IRA IRB 26543 bp each), large single-copy (LSC 80218 bp) small region (SSC 17598 bp). In total, 124 unique genes 82 protein-coding genes, 34 tRNA 8 rRNA were identified in P. genome. A total 61 long 290 SSRs detected It has typical 50 kb inversion 70 subtribe Phaseolinae. rpl16 , accD petB rsp16 clpP ndhA ndhF ycf1 coding regions found significant variation, intergenic trnk - rbcL atpB ndhJ rps4 psbD rpoB atpI atpA psbJ psbE psbB rsp11 rsp19 ccsA high degree divergence. phylogenetic analysis showed that appears be more closely related vulgaris V.unguiculata V. radiata . Conclusions characteristics time, these results will provide useful insights species identification, evolutionary studies molecular biology research.

Language: Английский

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Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

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

Published: June 7, 2022

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, wild resources jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences L. comparative analysis along with other species crucial pivotal to understanding evolution as well populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing revealed genome 151,884 bp, an ordinary quadripartite protected structure comprising 37.0% GC. Overall, 113 different genes recognized genome, consisting 30 distinct tRNA genes, four ribosomal RNAs 79 unique protein-encoding genes. Here, 3234 SSRs 2053 complex repeats identified, comprehensive performed for IR expansion contraction, codon usage bias. genome-wide sliding window variability rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, trnP-psaJ-rpl33 higher among 48 cp genomes, displaying nucleotide SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, ycf2 exhibit zero synonymous substitution, revealing divergence or restriction. Furthermore, out 78 protein-coding we found that accD rpl36 under positive selection: however, at entire-chloroplast protein scale, have gone through purifying selection. Also, new tree rebuilt, believe classification clearer than before. The provided here will aid future studies identification, population genetics, conservation.

Language: Английский

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