Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Год журнала: 2022, Номер 65(2), С. 299 - 323

Опубликована: Ноя. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Язык: Английский

---

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

---

GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data

Molecular Ecology Resources, Год журнала: 2024, Номер 24(3)

Опубликована: Янв. 10, 2024

Abstract The advancement of next‐generation sequencing (NGS) technologies has been revolutionary for the field evolutionary biology. This technology led to an abundance available genomes and transcriptomes researchers mine. Specifically, can mine various types molecular markers that are vital phylogenetic, ecological studies. Numerous tools have developed extract these from NGS data. However, due insufficient number well‐annotated reference non‐model organisms, it remains challenging obtain accurately efficiently. Here, we present GeneMiner, improved expanded version our previous tool, Easy353. GeneMiner combines reference‐guided de Bruijn graph assembly with seed self‐discovery greedy extension. Additionally, includes a verification step using parameter‐bootstrap method reduce pitfalls associated relatively distant reference. Our results, both experimental simulation data, showed acquire phylogenetic plants transcriptomic, genomic other is designed be user‐friendly, fast memory‐efficient. Further, compatible Linux, Windows macOS. All source codes publicly on GitHub ( https://github.com/sculab/GeneMine r) Gitee https://gitee.com/sculab/GeneMiner ) easy accessibility transparency.

Язык: Английский

---

Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 28, 2025

Due to its previously illicit nature, Cannabis sativa had not fully reaped the benefits of recent innovations in genomics and plant sciences. However, Canada's legalization C. products derived from flower 2018 triggered significant new demand for robust genotyping tools assist breeders meeting consumer demands. Early molecular marker-based research on focused screening sex chemotype, more has sought use markers target traits agronomic interest, study populations differentiate between cultivars. In this study, we have conducted whole genome sequencing 32 cultivars, mined data SNPs, developed a reduced SNP panel discriminate sequenced then validated 20-SNP using DNA cultivars tested assays commercially available dried flower. The assay conversion rate was higher extracted fresh material than samples. called genotypes were internally consistent, highlighting discrepancies detected observed assays. primary contributions work are clearly document process used develop minimal panels, feasibility such panels outline improvements goals future iterations PCR-based, enable efficient development identify screen Our key recommendations increase sampling density account intra-cultivar variability; leverage read length paired-end short-read technology; conduct in-depth pre- post-processing reads, mapping, variant calling data; integrate trait-associated loci multi-purpose panels; iterative approaches vitro validation ensure that only most discriminant performant SNPs retained.

Язык: Английский

---

Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Molecular Biology and Evolution, Год журнала: 2022, Номер 39(12)

Опубликована: Дек. 1, 2022

Abstract The Angiosperms353 gene set (AGS) consists of a 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover efficiently accurately from high-throughput sequences. Here, we developed Easy353, reference-guided assembly tool the AGS sequencing (HTS) data (including genome skimming, RNA-seq, target enrichment). Easy353 is an open-source user-friendly assembler diverse types data. It has graphical user interface command-line compatible with all widely-used computer systems. Evaluations, based on both simulated empirical data, suggest yields low rates errors.

Язык: Английский

---

Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae

Genome Biology and Evolution, Год журнала: 2023, Номер 15(3)

Опубликована: Фев. 24, 2023

Large genomic data sets are becoming the new normal in phylogenetic research, but identification of true orthologous genes and exclusion problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with through synteny a set 11 representative diploid Brassicaceae whole-genome sequences spanning entire space. Then, evaluated resulting gene regarding number, functional annotation, species tree resolution. Finally, syntenic for comparative genomics ancestral genome analysis. The use resulted considerably more orthologs also allowed us to reliably identify paralogs. Surprisingly, did not detect notable differences between trees reconstructed from other sets, including Angiosperms353 Brassicaceae-specific enrichment set. However, comprised multitude functions, strongly suggesting that this method marker selection phylogenomics suitable studies value downstream function analysis, interaction, network studies. present first reconstruction Core which predating lineage diversification ∼25 million years ago.

Язык: Английский

---

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(3), С. 546 - 578

Опубликована: Янв. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Язык: Английский

---

Target capture and genome skimming for plant diversity studies

Applications in Plant Sciences, Год журнала: 2023, Номер 11(4)

Опубликована: Июль 1, 2023

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such can still be difficult many plant species. For example, obtaining high-molecular-weight DNA is typically impossible samples historical herbarium collections, which often degraded DNA. The need to fast-freeze newly collected living conserve high-quality complicated when plants are only found remote areas. Therefore, short-read reduced-genome representations, as target capture genome skimming, remain important studies. Here, we review pros cons each technique non-model taxa. We provide guidance related logistics, budget, genomic resources previously available clade, nature study. Furthermore, assess bioinformatic analyses, detailing best practices pitfalls, suggest pathways combine generated with legacy data. Finally, explore possible downstream analyses allowed by type using technique. a practical guide help researchers make best-informed choice regarding reduced representation studies cases where remains impractical.

Язык: Английский

---

Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems

Applications in Plant Sciences, Год журнала: 2024, Номер 12(1)

Опубликована: Янв. 1, 2024

A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution genus to species especially in groups complicated by polyploidy hybridization.

Язык: Английский

---

Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data

Molecular Ecology Resources, Год журнала: 2022, Номер 22(8), С. 3018 - 3034

Опубликована: Июль 7, 2022

The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach detecting and utilizing them tree inference, by retrieving both ortho- paralogous copies creating orthologous alignments, from which the gene trees are built. implemented this ParalogWizard demonstrate its performance plant groups that underwent whole genome duplication relatively recently: subtribe Malinae (family Rosaceae), Angiosperms353 as well Malinae481 probes, genus Oritrophium Asteraceae), Compositae1061 Amomum Zingiberaceae), Zingiberaceae1180 probes. Discriminating between orthologues reduced discordance increased species support case Malinae, but not Amomum. This may relate to difference proportion loci sets, was highest Malinae. Overall, reconstruction following has potential increase reduce data, particularly if is high.

Язык: Английский

---