Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(8), P. 3161 - 3175

Published: July 5, 2022

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes genus a model testing efficacy super-barcodes. In this study, we generated multiple data sets comprising standard barcodes (matK, rbcL, trnH-psbA, nrITS) (plastid genome, nrDNA arrays) across 58 individuals from 12 out 13 China. No samples were correctly assigned using while only 27.27% with accessions distinguished plastid its partitioned sets-the lowest estimated rate super-barcode success literature so far. For other taxa similarly divergence low levels genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes failure. Taken together, our study suggests that by no means immune challenges imposed evolutionary complexity. We therefore call developing multilocus markers discrimination

Language: Английский

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Target capture and genome skimming for plant diversity studies

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 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.

Language: Английский

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AI-Powered IoT and UAV Systems for Real-Time Detection and Prevention of Illegal Logging

Results in Engineering, Journal Year: 2024, Volume and Issue: unknown, P. 103277 - 103277

Published: Oct. 1, 2024

Language: Английский

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Unlocking the geography of Azobé timber (Lophira alata): revealing spatial genetic structure beyond species boundaries

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: March 12, 2025

The illegal trade of tropical timber constitutes a major and persistent environmental problem. Since the detection fraud in documents remains challenging, forensic tools that can independently trace origin are needed. In this study, we evaluated potential chloroplast genome (plastome) as genetic tool to verify claimed species geographic from Azobé (Lophira alata), an intensively exploited threatened tree species. We sampled 480 trees Lophira alata congeneric L. lanceolata across nine countries Central West Africa. Sampling included 15 logging concessions Cameroon, Gabon Republic Congo. DNA was isolated cambium or leaf tissue, complete plastid genomes were assembled. A total 228 SNPs 436 retained, which formed 35 pDNA haplotypes (with length 179 SNPs). two shared one haplotype contained several closely related haplotypes. For alata, detected moderately strong correlation between spatial distances. Two widely spread core Africa, while others more spatially constrained endemic, for example, (potentially cryptic species) Northern distribution revealed clear structure. Some potentially hamper site distinction wood samples, but still reveal their wider region origin. regions where endemic present, differentiation may be successful at finer scales. Thus, resolution tracing vary regions. assembled first reference database plastome-wide SNP datasets timber, with focus on areas. Our work represents step towards plastome-based species, also reveals limited method differentiation. To validate tracing, further steps, including assignment blind sample tests, will

Language: Английский

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Genetics and Breeding of Fritillaria spp.

Published: Jan. 1, 2025

Language: Английский

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Reporting Complete Chloroplast Genome of Endangered Red Mulberry Useful for Understanding Hybridization and Phylogenetic Relationships

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Introgressive hybridization of the North American native red mulberry (Morus rubra) with its invasive congener white alba) has severely threatened genetic integrity M. rubra, which is primarily found in pristine riparian forests. The major objectives present study were 1) to sequence, assemble, and annotate complete chloroplast (cp) genome 2) perform phylogenomic analyses Morus species assess their evolutionary history events within genus. We sampled 45 trees representing populations from eight US states for cp sequencing. that rubra ranged 159,396 159,423 bp contained 128 genes coding rRNAs, 37 tRNAs, 83 proteins. was at least 103 larger than alba. cpDNA sequence polymorphism analysis showed presence 12 haplotypes. across Morus species identified trnK-UUU-rps16, psbI-trnG-UCC, psbC-psbZ, psbZ-trnM-CAU, rps4-trnT-UGU, trnT-UGU-trnL-UAA, ndhC-trnV-UAC, psbE-petL, clpP1, ndhF-rpl32, rpl32-trnL-UAG, ccsA-ndhDas having higher DNA (Pi > 0.01), making them candidate species-specific markers. Phylogenomic revealed distinct clades Asian, American, South African Morus, supporting monophyly Divergence time most common ancestor genus diverged 38.67 million years ago (MYA), separating clade M. mesozygia and insignis others, while Asian diverged 28.63 MYA. results this provide insights into structure rubra, offering foundational data addressing complex taxonomic complexities developing molecular markers population genetics, including introgressive hybridization.

Language: Английский

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Reporting complete chloroplast genome of endangered red mulberry, useful for understanding hybridization and phylogenetic relationships

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 18, 2025

Introgressive hybridization of the North American native red mulberry (Morus rubra) with its invasive congener white alba) has severely threatened genetic integrity M. rubra, which is primarily found in pristine riparian forests. The major objectives present study were (1) to sequence, assemble, and annotate complete chloroplast genome (2) perform phylogenomic analyses Morus species assess their evolutionary history events within genus. We sampled 45 trees representing populations from eight US states for sequencing. that rubra ranged 159,396 159,423 basepair (bp) contained 128 genes coding rRNAs, 37 tRNAs, 83 proteins. was at least 103 bp larger than alba. DNA sequence polymorphism analysis showed presence 12 haplotypes. across identified trnK-UUU-rps16, psbI-trnG-UCC, psbC-psbZ, psbZ-trnM-CAU, rps4-trnT-UGU, trnT-UGU-trnL-UAA, ndhC-trnV-UAC, psbE-petL, clpP1, ndhF-rpl32, rpl32-trnL-UAG, ccsA-ndhD as having higher (Pi > 0.01). Phylogenomic revealed distinct clades Asian, American, South African Morus, supporting monophyly Divergence time most recent common ancestor genus diverged 38.67 million years ago (MYA), separating clade mesozygia insignis others, while Asian 28.63 MYA. results this provide insights into structure offering a foundational data bridges knowledge gaps addressing complex taxonomic complexities developing molecular markers population genetics, including introgressive hybridization.

Language: Английский

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Timber traceability, determining effective methods to combat illegal logging in Africa: A review

Trees Forests and People, Journal Year: 2024, Volume and Issue: unknown, P. 100709 - 100709

Published: Oct. 1, 2024

Language: Английский

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Genetic characterization of a group of commercial African timber species: From genomics to barcoding

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(4), P. e0284732 - e0284732

Published: April 20, 2023

In the last decades, illegal logging has posed a serious threat for integrity of forest ecosystems and biodiversity conservation in tropical Africa. Although international treaties regulatory plans have been implemented to reduce logging, much total timber volume is harvested traded illegally from African regions. As result, development application analytical tools enhance traceability identification wood related products critical enforce regulations. Among available techniques, DNA barcoding promising approach molecular plant species. However, although it used successfully discrimination animal species, no set genetic markers universal this work, we firstly characterized diversity 17 highly-valuable species five genera ( Afzelia , Guibourtia Leplea Milicia Tieghemella ) across their distribution ranges West Central Africa using genome skimming order reconstruct chloroplast genomes nuclear ribosomal DNA. Next, identified single-nucleotide polymorphisms (SNPs) closely-related way, developed tested novel species-specific barcodes identification.

Language: Английский

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Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Biodiversity Data Journal, Journal Year: 2023, Volume and Issue: 11

Published: Oct. 27, 2023

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering window into the genetic past species often permitting access to information that can no longer be sampled wild. Due their age, preparation storage conditions, DNA retrieved from museum herbarium is poor yield, heavily fragmented biochemically modified. This not only poses methodological challenges recovering nucleotide sequences, but also makes such investigations susceptible environmental contamination. In this paper, we review practical associated with making recovery sequence data more routine. We first key operational principles issues address, guide decision-making process dialogue between researchers curators about when how sample analyses. then outline range steps taken reduce likelihood contamination including set-ups, workflows working practices. finish by presenting series case studies, each focusing on protocol practicalities application different mainstream methodologies including: (i) shotgun insect mitogenomes, (ii) whole genome insects, (iii) skimming recover plant plastid genomes specimens, (iv) target capture multi-locus nuclear sequences (v) RAD-sequencing bird (vi) ancient bovid bone samples.

Language: Английский

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