Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

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

Published: April 6, 2022

Abstract Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with center of diversity Africa. Previous studies on species this have not obtained complete chloroplast genomes, structures variations. Additionally, phylogenetic position Orchidaceae still controversial uncertain. Therefore, study, we sequenced plastomes six Kenya based genome skimming, subjected them to comparative genomic analysis, reconstructed relationships other species. Results The results exhibited that genomes had typical quadripartite structure conserved arrangement moderate divergence. ranged from 145,484 bp 149,274 length an almost similar GC content 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated inverted regions, 16 each possessd one or more introns. Although no structural variations were observed among plastomes, about 1 kb inversion was found modesta all 11 ndh lost pseudogenized. Comparative analysis overall sequence identity confirmed for both coding non-coding regions , SC exhibit higher variation than IRs. Furthermore, there various amplifications IR Most protein-coding these high degree codon preference. We screened out SSRs seven relatively highly variable loci. Moreover, 13 discovered significant positive selection. Phylogenetic showed formed monophyletic clade closely related tribe Vandeae. family inferred 85 sequences generally consistent previous robust. Conclusions Our study initial report species, elucidates characteristics filters can contribute development DNA markers use genetic variability evolutionary . strongly support part

Language: Английский

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Advances and prospects of orchid research and industrialization

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together human influences also make it a keystone group biodiversity conservation. The advent sequencing technologies transgenic techniques represents quantum leap orchid research, enabling molecular approaches to be employed resolve historically interesting puzzles basic applied biology. To date, 16 different genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, Orchidoideae) been released. genome projects given rise massive data greatly empowers studies pertaining key innovations evolutionary mechanisms for breadth species. extensive exploration transcriptomics, comparative genomics, recent advances gene engineering linked important traits orchids multiplicity regulating networks, providing great potential genetic enhancement improvement. In this review, we summarize progress achievement fundamental research industrialized application particular focus tools, future prospects breeding post-genomic comprehensive assemblage state art knowledge industrialization.

Language: Английский

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Common Methods for Phylogenetic Tree Construction and Their Implementation in R

Bioengineering, Journal Year: 2024, Volume and Issue: 11(5), P. 480 - 480

Published: May 11, 2024

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing trees, including distance methods, maximum parsimony, likelihood, Bayesian inference, tree-integration (supermatrix supertree). Here discuss advantages, shortcomings, applications of each method offer relevant codes to construct trees from molecular data using packages algorithms R. This review aims provide comprehensive guidance reference researchers seeking while also promoting further development innovation field. By offering clear concise overview different available, hope enable select most appropriate approach their specific research questions datasets.

Language: Английский

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Orchid conservation in China from 2000 to 2020: Achievements and perspectives

Plant Diversity, Journal Year: 2021, Volume and Issue: 43(5), P. 343 - 349

Published: June 22, 2021

We review achievements in the conservation of orchid diversity China over last 21 years. provide updated information on biodiversity and suggestions for China. outline national policies conservation, especially which general guidelines There are now approximately 1708 known species Orchidaceae 181 genera China, including five new 365 described The assessment risk extinction all 1502 native 2013 indicated that 653 were identified as threatened, 132 treated data-deficient, four endemic to classified extinct. Approximately 1100 (ca. 65%) protected nature reserves, another ~66 provincial reserves. About 800 have living collections major botanical gardens. pollination biology 74 genetic spatial structure 29 been investigated at a local scale and/or across distributions. mycorrhizal fungal community composition has many genera, such Bletilla, Coelogyne, Cymbidium, Cypripedium, Dendrobium. 292 will be included list key wild plants this year. Two tasks near future include situ monitoring population dynamics endangered species.

Language: Английский

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Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 60(6), P. 1263 - 1280

Published: June 17, 2021

Abstract The olive genus Olea includes c . 30–40 taxa in three subgenera ( , Tetrapilus and Paniculatae ) within the family Oleaceae. Historically, was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus poor resolution clades. These analyses also showed not monophyletic. Reliable identification species is important for both their conservation utilization this economically genus. In study, we used phylogenomic data from genome skimming to resolve relationships identify molecular markers identification. We assembled complete plastomes, nrDNA 26 individuals representing 13 using next‐generation sequencing added 18 publicly available accessions developed nuclear SNPs infer phylogenetic Large‐scale 138 samples tribe Oleeae polyphyly with caudatilimba sharing most recent common ancestor main clade (subgenus ). interspecific owing a possible rapid radiation. By comparing plastome data, identified ycf1 b psbE‐petL as best ‐specific chloroplast DNA barcodes. Compared universal barcodes, specific barcodes super‐barcode exhibited higher discriminatory power. Our results demonstrated power phylogenomics improve intricate provided new insights allow accurate species.

Language: Английский

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Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

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

Published: Jan. 7, 2021

Abstract Background Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. species are found on all continents of the Northern Hemisphere, and East Asia hosts highest number Morphological characters such as fruit anatomy, leaf morphology subterranean structures show extreme diversity. Consequently, taxonomic classification complex remains controversial, classifications proposed by previous studies based morphological data molecular highly discordant. In addition, phylogenetic relationships major clades in group, particularly s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used for evaluating genetic Results this study, we sequenced assembled 28 complete cp genomes from 22 species, two varieties cultivars . Combined with 36 available GenBank representative subfamily Apioideae, characteristics evolutionary patterns were studied, resolved. The had typical quadripartite structure including a pair inverted repeats (IRs: 5836–34,706 bp) separated large single-copy region (LSC: 76,657–103,161 small (SSC: 17,433–21,794 bp). Extensive expansion contraction IR observed among pattern diversification showed high consistency placement Species grouped into clades, most group A. omeiensis sinensis Sinodielsia Ligusticum tenuissimum. Conclusions Our results further demonstrate power plastid phylogenomics enhancing reconstructions genera provide new insights plastome evolution across

Language: Английский

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Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: June 27, 2023

The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. structural characterization complete chloroplast genomes P. storbatiana wilsonii were analyzed compared with those related taxa provide a better understanding their genomic information on phylogeny.It was shown that had typical quadripartite structure conserved genome arrangements moderate divergence. 145,885 bp 145,445 in length, respectively, shared similar GC content 36.8%. Gene annotations two revealed 109 single-copy genes consistently. In addition, 20 duplicated the inverted regions, 16 each possessed one or more introns, five ndh (NA (D)H dehydrogenase) observed both. Comparative analysis total cp other six confirmed stable sequence identity coding non-coding regions higher variation SC than IR regions. Most protein-coding high degree codon preference. Moreover, 45 discovered positive selection. However, different amplifications these eight species. Phylogenetic based CDS from 60 representing main clades Orchidaceae indicated including stobartiana formed monophyletic clade bootstrap nested tribe Vandeae Epidendroideae, consistent previous studies.The results could insight into plastome evolution phylogenetic relationships Phalaenopsis.

Language: Английский

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Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(13), P. 11167 - 11167

Published: July 6, 2023

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains number ornamental species. However, there is no information on chloroplast genomes which limits our studies this genus. In study, we reported three species Paraphalaenopsis (P. labukensis, P. denevel, and laycockii ‘Semi-alba’) performed comprehensive comparative analysis. These showed typical quadripartile structure. Their lengths ranged 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding 38 tRNA 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence genomes. addition, six hypervariable regions were identified (psbM-trnDGUC, psbB, ccsA, trnKUUU, trnSGCU-trnGUCC, rps16-trnQUUG) that can be used as DNA molecular markers. Phylogenetic relationships determined using 28 12 genera Aeridinae. Results suggested was clade Aeridinae sister Holcoglossum-Vanda clade, with 100% bootstrap support within The findings study provided foundation for future phylogenetic

Language: Английский

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Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(3), P. 1578 - 1578

Published: Jan. 27, 2024

Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic fully mycoheterotrophic plant. Given special nutritional strategies evolutionary significance, mitogenome was first characterized, three plastomes sampled from Asia were assembled. The found be smallest among Orchidaceae, with lengths ranging 18,339 19,047 bp, exhibited high sequence variety. For mitogenome, total 414,552 bp in length, comprising 26 circular chromosomes, identified. A 54 genes, including 38 protein-coding 13 tRNA 3 rRNA annotated. Multiple repeat sequences spanning length 203,423 (45.47%) discovered. Intriguingly, six plastid regions via intracellular gene transfer four horizontal observed. phylogenomics, incorporating 90 56 mitogenomes, consistently revealed sister relationship Gastrodia, bootstrap percentage 100%. These findings shed light on organelle evolution Orchidaceae plants.

Language: Английский

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The Complete Chloroplast Genomes of Bulbophyllum (Orchidaceae) Species: Insight into Genome Structure Divergence and Phylogenetic Analysis

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(5), P. 2665 - 2665

Published: Feb. 25, 2024

is one of the largest genera and presents some most intricate taxonomic problems in family Orchidaceae, including species ornamental medical importance. The lack knowledge regarding characterization

Language: Английский

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