Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets DOI Creative Commons
Xueqin Wang, Tao Xiong, Yiying Wang

et al.

Horticulture Advances, Journal Year: 2024, Volume and Issue: 2(1)

Published: Jan. 29, 2024

Abstract Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization enrichment (Hyb-seq) is innovative and flexible, then HTS strategy widely adopted The universal Angiosperms353 probe sets (Angiosperms353) are instrumental Hyb-seq been witnessed increased application recent years. This review integrates numerous publications empirical datasets to comprehensively assess the potential applications Angiosperms353. Through evaluations using 18-taxa 343-taxa genomic datasets, this explores factors influencing gene capture. RNA-seq yielded highest number genes, followed by whole-genome genome skimming. Increased depth enhanced yields, no evident bias was observed across all tested angiosperm groups. In genomics era extensive data, provides comprehensive guidelines for practical Angiosperms353, promoting resource recycling maximizing data sharing utilization.

Language: Английский

Specimen Identification Through Multilocus Species Tree Constructed From Single‐Copy Orthologs (SCOs): A Case Study in Cymbidium Subgenus Jensoa DOI Creative Commons
Zhengshan He, Junxing Yang, Jialin Huang

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Standard barcodes and ultra‐barcode encounter significant challenges when delimiting discriminating closely related species characterized by deep coalescence, hybrid speciation, gene flow, or low sequence variation. Single‐copy orthologs (SCOs) have been widely recognized as standardized nuclear markers in metazoan DNA taxonomy, yet their application plant taxonomy remains unexplored. This study evaluates the efficacy of SCOs for identifying recently diverged within Cymbidium subgenus Jensoa , where ultra‐barcodes previously shown limited resolution. Remarkably, over 90% 9094 targeted reference SCOs, inferred from three genomes, were successfully retrieved all 11 representative subg. using ALiBaSeq at a minimal 5× depth whole genome shotgun sequences. The tree, reconstructed multiple refined SCO matrices under coalescent model, effectively distinguished identified mislabeled misidentified specimens. comprehensive produced our pipeline not only enhance phylogenetic analysis but also improve precision diagnosis. Additionally, biparentally inherited serving multi‐locus markers, augment effectiveness barcoding support transition to multi‐locus, species‐tree‐based specimen assignment strategies.

Language: Английский

Citations

0
Plant DNA barcode library for native flowering plants in the arid region of northwestern China DOI
Feng Song, Ting Li, Hai‐Fei Yan

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(6), P. 1389 - 1402

Published: April 6, 2023

DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable traceable barcode reference library with extensive coverage necessary but unavailable many geographical regions. The arid region in northwestern China, vast area of about 2.5 million km2 , ecologically fragile often overlooked studies. In particular, data from the China are lacking. We develop evaluate efficacy an native flowering plants China. Plant specimens were collected, identified vouchered this purpose. database utilized four markers, namely rbcL, matK, ITS ITS2, 1816 accessions (representing 890 385 genera 72 families), consisted 5196 sequences. Individual barcodes varied resolution rates: species- genus-level rates ITS2 79.9%-51.1%/76.1%, 79.9%-67.2%/88.9%, 85.0%-72.0%/88.2% 81.0%-67.4%/84.9%, respectively. three-barcode combination rbcL + matK (RMI) revealed higher (75.5%/92.1%, respectively). total 110 plastomes newly generated as super-barcodes to increase seven species-rich genera, Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene Zygophyllum. Plastomes compared standard their combination. suggest future databases include super-barcodes, especially complex genera. plant current study provides valuable resource biological investigations regions

Language: Английский

Citations

10
Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya–Hengduan Mountains and adjacent regions DOI
Yanyan Liu,

Jia-Liang Cao,

Shenglong Kan

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 193, P. 108023 - 108023

Published: Feb. 10, 2024

Language: Английский

Citations

3
An Integrative Framework Reveals Widespread Gene Flow During the Early Diversification of Malvaceae S.L DOI
Weilong Yang, Pei‐Feng Liu, Jacob B. Landis

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes DOI Creative Commons
Peng Sun, Yu Yang, Ming Yuan

et al.

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 14, 2025

Over the past decade, continuous and rapid advances in bioinformatics have led to an increasingly common use of molecular sequence comparison for phylogenetic analysis. However, multi-software cross-platform strategies has increased complexity tree estimation. Therefore, development application streamlined analysis tools are growing significance field biology. Particularly genomes with relatively short sequences, there is a lack simple integrative In this study, we present CamlTree (Concatenated alignments maximum-likelihood tree), user-friendly desktop software designed simplify viral mitochondrial genomes, ultimately facilitating related research. provides workflow including gene concatenation (or coalescence), alignment, alignment optimization, estimation trees using both (ML) Bayesian inference (BI) methods. was written TypeScript developed Electron framework. It offers primarily interface based on React been released Windows OS. integrates several popular optimize process estimating polygenic trees. The establishment can assist researchers reducing their workload enhancing data processing efficiency, enabling them expedite research progress. software, along detailed user manual, available at https://github.com/BioCrossCoder/camltree .

Language: Английский

Citations

0
Phylogenomics provides new Insight into the phylogeny and diversification of Asian Lappula (Boraginaceae) DOI Creative Commons
Danhui Liu,

Quan‐Ru Liu,

Komiljon Tojibaev

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 208, P. 108361 - 108361

Published: April 25, 2025

The application of omics data serves as a powerful tool for investigating the roles incomplete lineage sorting (ILS) and hybridization in shaping genomic diversity, offering deeper insights into complex evolutionary processes. In this study, we utilized deep genome sequencing from 76 individuals Lappula its closely allied genera, collected China Central Asia. By employing HybPiper Easy353 pipelines, recovered 262-279 single-copy nuclear genes (SCNs) 352-353 Angiosperms353 genes, respectively. We analyzed multiple datasets, including complete chloroplast genomes filtered set 475 SCNs, to conduct phylogenetic analyses using both concatenated coalescent-based methods. Furthermore, employed Quartet Sampling (QS), coalescent simulations, MSCquartets, HyDe, reticulate network investigate sources discordance. Our results confirm that is polyphyletic, with L. mogoltavica clustering Pseudolappula sinaica forming sister relationship other taxa included study. Additionally, three Lepechiniella nested within distinct clades Lappula. Significant gene tree discordance was observed at several nodes Coalescent simulations hybrid detection suggest ILS contribute these discrepancies. Flow cytometry (FCM) confirmed presence diploid tetraploid Phylogenetic further revealed Clades IV VII likely originated through hybridization, tetraploids Clade arising two independent events. "ghost lineage" identified redowskii one donors allopolyploidization. conclusion, our study provides new relationships Asian contributing more comprehensive understanding evolution diversification

Language: Английский

Citations

0
Climatic niche divergence and long-distance dispersal contributed to the pantropical intercontinental disjunctions of a liana lineage (Uncaria, Rubiaceae) DOI Creative Commons
Xianhan Huang,

Jing-Yi Peng,

Nan Lin

et al.

Plant Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

Citations

0
Chloroplast Genomes and Phylogenetic Analysis of Three Carthamus (Asteraceae) Species DOI Open Access
Tiange Yang,

Saimire Aishan,

Jiale Zhu

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(21), P. 15634 - 15634

Published: Oct. 26, 2023

The genus Carthamus Linnaeus, which belongs to the tribe Cardueae in Asteraceae family, originated Mediterranean region and consists of approximately 20 species worldwide. Understanding phylogeny is crucial for cultivation C. tinctorius. Although chloroplast genomes are widely used identification evolutionary studies, there have been limited investigations on species. In this study, we assembled persicus, tinctorius × lanatus combined them with five comparative genomic analysis. sizes lanatus, persicus were 152,602 bp, 153,177 respectively. Comparative analysis showed that genome structures four highly conserved. Additionally, phylogenomic demonstrated plastid angiosperms353 dataset significantly improved phylogenetic support This supported as a monophyletic taxon its internal division into sect. Atractylis. was closely related Carduncellus, Femeniasia, Phonus, Centaurea. conclusion, study not only expands our understanding cp but also provides more comprehensive studies Carthamus.

Language: Английский

Citations

8
The complete chloroplast genome of rhododendron williamsianum (ericaceae) DOI Creative Commons

Daoyuan Zhou,

Juan Wang,

Fengjuan Zhou

et al.

Mitochondrial DNA Part B, Journal Year: 2024, Volume and Issue: 9(8), P. 1058 - 1062

Published: Aug. 2, 2024

Rehder & E. H. Wilson 1913, is a plant with important horticultural value. Here we report its chloroplast genome. The total length of the genome was 205,424 bp, GC content 35.8%. It consisted 107,968 bp large single copy, 2606 small and pair 47,425 inverted repeats separating them. Within genome, there were 110 unique genes, which included 76 protein-coding 4 rRNA 30 tRNA genes. Our phylogenetic analyses indicated that

Language: Английский

Citations

2
Backbone phylogeny of Salix based on genome skimming data DOI Creative Commons
Kaiyun Chen,

Jin-Dan Wang,

Rui-Qi Xiang

et al.

Plant Diversity, Journal Year: 2024, Volume and Issue: 47(2), P. 178 - 188

Published: Sept. 13, 2024

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy systematics extremely difficult relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, single-copy orthologs (SCOs) from 66 accessions, along publicly available sequence read archive (SRA) datasets to obtain robust backbone phylogeny Salix, clarify its gain more precise understanding origin diversification species-rich genus. SCO resolved into two clades, plastome-based phylogenies lacking inner resolution offering fully phylogenies. Our results support classification five subgenera: Urbaniana, Triandrae, Longifoliae Vetrix. We observed significant acceleration in rate within Chamaetia-Vetrix clade, while exhibited increased rates spanning early Oligocene late Miocene. These changes coincided contemporaneous tectonic climate change events. provide foundation for future systematic evolutionary studies Salix. Additionally, showed that genome skimming data an efficient, rapid, reliable approach obtaining extensive genomic phylogenomic studies, enabling comprehensive elucidation relationships.

Language: Английский

Citations

2