Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Genome biology, Journal Year: 2016, Volume and Issue: 17(1)

Published: June 23, 2016

Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from variety land plants has enhanced our understanding biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which transgenes can be engineered to enhance plant agronomic traits or produce high-value agricultural biomedical products. In this review, we discuss impact genome sequences origins economically important cultivated species changes that have taken place during domestication. We also potential biotechnological applications genomes.

Language: Английский

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A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

Systematic Biology, Journal Year: 2018, Volume and Issue: 68(4), P. 594 - 606

Published: Dec. 7, 2018

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds nuclear loci phylogeny reconstruction. Much the cost developing targeted sequencing approaches associated with generation preliminary needed identification orthologous probe design. In plants, identifying has proven difficult due to a large number whole-genome duplication events, especially in angiosperms (flowering plants). We used multiple alignments over 600 353 putatively single-copy protein-coding genes identified by One Thousand Plant Transcriptomes Initiative design set probes phylogenetic studies any angiosperm group. To maximize potential probes, while minimizing production, we introduce k-medoids clustering approach identify minimum sequences necessary represent each coding final set. Using this method, 5–15 representative were selected per locus, representing diversity more efficiently than if designed using available sequenced genomes alone. test our approximately 80,000 hybridized 42 species spanning all higher-order groups angiosperms, focus on taxa not present probes. Out possible sequences, recovered average 283 at least 100 species. Differences among recovery could be explained relatedness design, suggesting that there no bias Our set, which 260 kbp sequence, achieved median 137 taxon regions, maximum 250 kbp, additional 212 flanking non-coding regions across These results suggest Angiosperms353 described here effective group flowering plants would useful level groups, including entire clade itself.

Language: Английский

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Volatile Compounds in Citrus Essential Oils: A Comprehensive Review

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: Feb. 4, 2019

The essential oil fraction obtained from the rind of Citrus spp is rich in chemical compounds interest for food and perfume industries, therefore has been extensively studied during last decades. In this manuscript we provide a comprehensive review volatile composition extracts ten most species: C. sinensis (sweet orange), reticulata (mandarin), paradisi (grapefruit), grandis (pummelo), limon (lemon), medica (citron), aurantifolia (lime), aurantium (bitter bergamia (bergamot orange) junos (yuzu). Forty-nine organic have reported all species, them terpenoid (90%), although about half identified peel are non-terpenoid. Over 400 volatiles different nature exclusively described only one these species some could be useful as biomarkers. A hierarchical cluster analysis based on arranges three clusters which essentially mirrors those with genetic information. first comprised by reticulata, grandis, sinensis, aurantium, mainly characterized presence larger abundance non-terpenoid ester aldehyde than other reviewed. second junos, medica, bergamia, prevalence mono- sesquiterpene hydrocarbons. Finally, shows particular profile sulfur monoterpenoids esters aldehydes part its main differential peculiarities. systematic description each provided together general comparison leaves blossoms. Additionally, widely used techniques extraction also described.

Language: Английский

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Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

Molecular Biology and Evolution, Journal Year: 2016, Volume and Issue: unknown, P. msw242 - msw242

Published: Nov. 16, 2016

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, provide foods humans other animals, with many morphological types important ecological agricultural implications. Rosaceae is a family ∼3000 species an extraordinary spectrum distinct fruits, including fleshy peach, apple, strawberry prized their consumers, as well dry achenetum follicetum features facilitating seed dispersal, excellent for studying fruit evolution. To address evolution questions, we generated 125 new transcriptomic genomic datasets identified hundreds nuclear genes reconstruct well-resolved phylogeny highly supported monophyly all subfamilies tribes. Molecular clock analysis revealed estimated age ∼101.6 Ma crown divergence times tribes genera, providing geological climate context Phylogenomic yielded strong evidence numerous whole genome duplications (WGDs), supporting hypothesis that apple tribe had WGD revealing another one shared fruit-bearing members this tribe, moderate support WGDs in peach groups. Ancestral character reconstruction supports independent origins fruits from dry-fruit ancestors, drupes (e.g., peach) pomes apple) follicetum, drupetum (raspberry blackberry) achenetum. We propose environmental factors, Rosaceae, which foundation understanding

Language: Английский

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Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species

Frontiers in Plant Science, Journal Year: 2016, Volume and Issue: 07

Published: June 28, 2016

Quercus is considered as one of the most important genera in Northern Hemisphere its economic and ecological importance. Oaks are taxonomically perplexing due to interspecific shared morphological traits intraspecific variation, which mainly attributed hybridization. Universal plastid markers could not provide sufficient variable sites explore phylogeny this genus chloroplast genome-scale data proved be useful resolve intractable phylogenetic relationships. In study, four complete genomes species were sequenced published Q. baronii was retrieved for comparative analyses. The sizes these five ranged from 161,072 bp (Q. baronii) 161,237 dolicholepis), has been identified gene organization, order GC content similar other Fagaceae species. We analyzed nucleotide substitution, indels repeats genomes. detection 19 relatively highly regions provides potential further taxonomic study within Quercus. future observed that 4 genes (ndhA, ndhK, petA ycf1) subjected positive selection. Finally, relationships inferred obtained moderate-to-high supports, indicating genome may genus.

Language: Английский

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Practical considerations for plant phylogenomics

Applications in Plant Sciences, Journal Year: 2018, Volume and Issue: 6(3)

Published: March 1, 2018

The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. development of high‐throughput sequencing long‐read technologies ushered the era phylogenomics, where hundreds thousands nuclear genes whole organellar genomes are routinely used reconstruct evolutionary relationships. As result, understanding which options best suited for particular set questions can be difficult, especially those just starting field. Here, we review most recent advances plant phylogenomic methods make recommendations project‐dependent practices considerations. We focus on costs benefits different approaches regard information they provide researchers address. also highlight unique challenges opportunities systems, such as polyploidy, reticulate evolution, use herbarium materials, identifying optimal methodologies each. Finally, draw attention lingering field reusability sets, look at some up‐and‐coming that may help propel even further.

Language: Английский

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Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers

Annals of Botany, Journal Year: 2016, Volume and Issue: 117(4), P. 565 - 583

Published: March 4, 2016

The origin of limes and lemons has been a source conflicting taxonomic opinions. Biochemical studies, numerical taxonomy recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata,C. maxima,C. medica C. micrantha). However, the most remains controversial or unknown. aim this study was to perform extended analyses diversity, genetic structure lemons.The based on 133 accessions. It combined maternal phylogeny mitochondrial chloroplastic markers, nuclear analysis evaluation ploidy level use 123 including 73 diagnostic single nucleotide polymorphism (SNP) indel markers.The lime lemon horticultural group appears be highly polymorphic, with diploid, triploid tetraploid varieties, many independent reticulation events which defined sub-groups. Maternal involves cytoplasmic types out six encountered in genus. All accessions were heterozygous, admixture two, three even ancestral genomes. Molecular varieties same sub-group very low.Citrus contributed all direct male parent for main sub-groups combination micrantha close papeda (for aurata, excelsa, macrophylla aurantifolia--'Mexican' Tanaka's taxa), reticulata(for limonia, karna jambhiri taxa, popular citrus rootstocks such as 'Rangpur' lime, 'Volkamer' 'Rough' lemons), aurantium limetta limon--yellow types--varieties taxa) maxima × reticulate hybrid limettioides--'Palestine sweet' types--and meyeri). Among limes, latifolia ('Tahiti' 'Persian' types) fertilization haploid ovule limon by diploid gamete aurantifolia, while aurantifolia ('Tanepao' 'Madagascar' lemon) probably an backcross (a fertilized medica). As vegetatively propagated (apomixis, practices) intra-sub-group phenotypic diversity results asexual variations.

Language: Английский

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Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(11), P. 1964 - 1975

Published: Oct. 2, 2023

Language: Английский

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Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: Jan. 15, 2018

The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of People's Republic China, bulbs 11 species are used in Chinese herbal medicines. However, traditional methods morphological classification cannot accurately identify closely related Fritillaria. Previous studies have attempted to these with universal molecular markers, but insufficient phylogenetic signal was available. this study, complete chloroplast genomes eight were compared. length ranges from 151,009 bp 152,224 bp. A total 136 SSR loci identified, including 124 polymorphic loci. For large repeat sequences, 108 and four types repeats observed. Ten highly variable regions identified as potential markers. These SSRs, sequences provide important information for development genetic markers DNA fingerprints. Phylogenetic analyses showed that topological structures all data sets (except IR regions) agreement well resolved. Overall, study provides comprehensive genomic resources, which will be valuable future evolution identification

Language: Английский

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Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

International Journal of Molecular Sciences, Journal Year: 2018, Volume and Issue: 19(3), P. 716 - 716

Published: March 2, 2018

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch monocotyledons. This contains a number economically-important horticulture and flowering plants. However, limited availability genomic information largely hindered study molecular evolution phylogeny Orchidaceae. In this study, we determined evolutionary characteristics whole chloroplast (cp) genomes phylogenetic relationships We firstly characterized cp four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, Platanthera japonica. The size genome ranged from 153,629 bp (C. davidi) to 160,427 (E. mairei). gene order, GC content, compositions are similar those other previously-reported angiosperms. identified that genes ndhC, ndhI, ndhK were lost in C. ndh I was P. japonica E. mairei. addition, types repeats (forward, palindromic, reverse, complement repeats) examined species. mairei had highest (81), while davidii lowest (57). total Simple Sequence Repeats at least 50 and, most, 78 Interestingly, 16 with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, ycf4 genes), which might play important role species' adaptation diverse environments. Additionally, 11 mutational hotspot regions determined, including five non-coding (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, ndhF-rpl32) six coding (rps16, ndhK, ndhF). analysis based on showed appendiculata closely related striata var. vreelandii, triplicate formed small monophyletic clade high bootstrap support. subfamilies Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, Vanilloideae, nested relationship tree. These results provide insights into adaptive

Language: Английский

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