Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Journal of Systematics and Evolution, Год журнала: 2021, Номер 59(5), С. 1124 - 1138

Опубликована: Июль 21, 2021

Abstract With the decreasing cost and availability of many newly developed bioinformatics pipelines, next‐generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming been widely used to obtain high‐copy fractions genomes, including plastomes, mitochondrial DNA (mtDNA), nuclear ribosomal (nrDNA). In this study, through simulations, we evaluated optimal (minimum) depth performance for recovering single‐copy genes (SCNs) from genome data, by subsampling resequencing data generating 10 sets with different coverage silico . We tested four (plastome, nrDNA, mtDNA, SCNs) obtained based on phylogenetic analyses Vitis clade at genus level Vitaceae family level, respectively. Our results showed that minimum high‐quality SCNs assembly via was about 10× coverage. Without steps synthesizing baits enrichment experiments, coupled incredibly low costs, showcase deep (DGS) is as effective capturing large Hyb‐Seq approach, addition entire nrDNA repeats. DGS may serve an efficient economical alternative be superior popular target enrichment/Hyb‐Seq approach.

Язык: Английский

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Corncob flower, Magnolia mixteca (M. sect. Macrophylla, Magnoliaceae) a new species endemic to the Alto Balsas Basin (Baja Mixteca), in the Pacific slopes of Oaxaca, Mexico

Phytotaxa, Год журнала: 2021, Номер 522(3), С. 200 - 210

Опубликована: Окт. 11, 2021

We describe and illustrate Magnolia mixteca, a new species of sect. Macrophylla from the Alto Balsas Basin in Oaxaca, Mexico, providing information about its ecology, biogeography conservation status. mixteca differs M. nuevoleonensis having larger flowers, longer petals, yellow petal-blotch, tan-sand coloured ovary more numerous stamens carpels. In addition, we provide distribution map key to Macrophylla. The relict this allows us consider it endangered (E).

Язык: Английский

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Prediction of potentially suitable areas for the introduction of Magnolia wufengensis under climate change

Ecological Indicators, Год журнала: 2021, Номер 127, С. 107762 - 107762

Опубликована: Май 1, 2021

Magnolia wufengensis, a new species of the subgenus Magnolia, has extremely high ornamental and scientific value due to its rich morphological diversity. The wild population M. wufengensis narrow habitat sparse population, is in critically endangered state. Currently, potential suitable areas for introduction limiting factors affecting distribution response global warming are unclear. Hence, an optimized MaxEnt model ENMeval package based on 49 occurrence records 16 environmental variables were used simulate under current future (2041–2080) climate change scenarios, including four representative concentration pathways (RCP2.6, RCP4.5, RCP6.0 RCP8.5), provide basis precise introduction, cultivation expansion wufengensis. was highly accurate, with average training area curve (AUC) 0.9895 ± 0.0011 after 10 repetitions. results indicated that mean temperature coldest quarter (-6.75–14.31 °C), diurnal range (≤14.29 min month (-13.73–10.77 warmest (≥12.93 precipitation wettest (40.99–715.42 mm) annual (4.47–24.56 °C) most important (threshold) In climate, 146.15 × 104 km2, 119.88 km2 224.87 projected as high, medium, low suitability respectively. These mainly located eastern central Asia, Mediterranean coast southern Europe, western America. Under change, world will be greatly reduced, degree fragmentation increase. addition, reduction different classes approximately 4.75%-39.14%, America Europe disappear, centroids tends shift northeast.

Язык: Английский

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

Journal of Systematics and Evolution, Год журнала: 2021, Номер 60(6), С. 1263 - 1280

Опубликована: Июнь 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.

Язык: Английский

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The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled size of was 1.84 Gb, contig N50 ca. 45 Mb scaffold 92 Mb. Identified repeats constituted approximately 57% genome, 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that magnolias form sister clade eudicots order Ceratophyllales, while monocots are other core angiosperms. our total 21 individuals 5 remnant populations as well 22 specimens belonging 8 related Magnoliaceae species, resequenced. results showed had higher genetic diversity (θw = 0.01126 θπ 0.01158) than species in Magnoliaceae. However, population structure suggested differentiation among very low. Analyses demographic history using different models consistently revealed 2 bottleneck events occurred. contemporary effective estimated be 10.9. patterns loads (inbreeding numbers deleterious mutations) constructive strategies conservation these sinica. Overall, will valuable genomic resource

Язык: Английский

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Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World

PhytoKeys, Год журнала: 2024, Номер 242, С. 161 - 227

Опубликована: Май 31, 2024

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for apple tribe Maleae, deficiency attributed to limited taxon and marker sampling. We conducted an extensive sampling, incorporating 563 plastomes from diverse range 370 species encompassing 26 presently recognized genera. Employing inference methods, including RAxML IQ-TREE2 Maximum Likelihood (ML) analyses, we established robust framework Maleae tribe. Our phylogenomic investigations provided compelling support three major clades within Maleae. By integrating nuclear data with morphological chromosomal evidence, propose updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, Lindleyinae Vauqueliniinae B.B.Liu (

Язык: Английский

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Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia s.l. (Magnoliaceae)

Journal of Systematics and Evolution, Год журнала: 2021, Номер 60(1), С. 1 - 15

Опубликована: Янв. 15, 2021

Abstract Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers genera and monogeneric Liriodendroideae Liriodendron L. This family occupies a pivotal phylogenetic position important insights into the diversification shows intercontinentally disjunct distribution patterns between eastern Asia Americas. Widespread morphological homogeneity slow substitution rates Magnolia s.l. resulted poorly supported relationships based on morphology or molecular evidence, which hampers our understanding genus’ temporal spacial evolution. Here, newly generated genome skimming data for 48 species, we produced robust phylogenies using genome‐wide markers from both plastid genomes single nucleotide polymorphism data. Contrasting nuclear revealed extensive cytonuclear conflicts shallow deep relationships. ABBA‐BABA PhyloNet analyses suggested hybridization occurred within sect. Yulania , is concordance ploidy level these sections. Divergence time estimates biogeographic reconstruction indicated that timing three tropical disjunctions coincided mid‐Eocene cooling climate and/or late Eocene deterioration, temperate much later, possibly during warm periods Miocene, hence supporting boreotropical flora concept

Язык: Английский

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Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade

Frontiers in Plant Science, Год журнала: 2022, Номер 12

Опубликована: Янв. 25, 2022

Plant biologists have debated the evolutionary origin of apple tribe (Maleae; Rosaceae) for over a century. The "wide-hybridization hypothesis" posits that pome-bearing members Maleae (base chromosome number x = 17) resulted from hybridization and/or allopolyploid event between progenitors other tribes in subfamily Amygdaloideae with 8 and 9, respectively. An alternative "spiraeoid proposed 17 arose via genome doubling 9 ancestors to 18, subsequent aneuploidy resulting 17. We use publicly available genomic data-448 nuclear genes complete plastomes-from 27 species representing all major within investigate relationships containing tribe. Specifically, we network analyses multi-labeled trees test competing wide-hybridization spiraeoid hypotheses. Hybridization occurred an ancestor Spiraeeae (x 9) clade Sorbarieae + Exochordeae 8) Kerrieae 9), giving rise Gillenieae 17). distantly related (i.e., supporting wide hypothesis). However, some evidence supports aspect hypothesis-the involved were likely both so was followed by result observed Maleae. By synthesizing existing data novel analyses, resolve nearly century-old mystery regarding Our results also indicate gene tree-species tree conflict cytonuclear are pervasive at several nodes Rosaceae.

Язык: Английский

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Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae)

BioMed Research International, Год журнала: 2022, Номер 2022, С. 1 - 13

Опубликована: Фев. 24, 2022

The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and Mediterranean region. phylogeny evolutionary history this are not clear. Knowledge phylogenetic relationships method for identification will be critical evolution genus. In study, we sequenced chloroplast genome 17 samples added additional sequences from GenBank. data were used to investigate evolution, infer relationships, access rate within Styrax. contains typical quadripartite structures, ranging 157,641 bp 159,333 bp. 114 unique genes. P distance among ranged 0.0003 0.00611. Seventeen small inversions SSR sites discovered genome. By comparing with sequences, six mutation hotspots identified, markers ycf1b trnT-trnL identified as best Styrax-specific DNA barcodes. specific barcodes superbarcode exhibited higher discriminatory power than universal Chloroplast phylogenomic results improved resolution compared previous analyses.

Язык: Английский

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Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses

Plant Diversity, Год журнала: 2023, Номер 45(4), С. 397 - 408

Опубликована: Апрель 6, 2023

is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36

Язык: Английский

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