New targets acquired: Improving locus recovery from the Angiosperms353 probe set

McLay, Todd G. B.; Birch, Joanne L.; Gunn, Bee F.; Ning, Weixuan; Tate, Jennifer A.; Nauheimer, Lars; Joyce, EM; Simpson, Lalita; Schmidt‐Lebuhn, Alexander N.; Baker, William J.; Forest, Félix; Jackson, Chris

doi:10.1002/aps3.11420

Cited by 51 publications

(31 citation statements)

References 47 publications

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“…Reads were first cleaned with Trimmomatic to remove barcode and adapter sequences and to remove reads with a quality score below 10 or reads less than 40 bp long ( Bolger et al, 2014 ). Cleaned reads were assembled into genes using the HybPiper assembly pipeline ( Johnson et al, 2016 ) using the expanded Angiosperms353 reference file ( McLay et al, 2021 ). In short, this pipeline first maps reads to the reference file using bwa ( Li and Durbin, 2009 ) and assembles reads into contigs using SPAdes ( Bankevich et al, 2012 ; Prjibelski et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

Simões

Eserman²,

Zuntini

et al. 2022

Front. Plant Sci.

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Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or a single nuclear region, have provided a framework for systematic studies of the family, but uncertainty remains at the level of the relationships among subfamilies, tribes, and genera, hindering evolutionary inferences and taxonomic advances. One of the enduring enigmas has been the relationship of Cuscuta to the rest of Convolvulaceae. Other examples of unresolved issues include the monophyly and relationships within Merremieae, the “bifid-style” clade (Dicranostyloideae), as well as the relative positions of Erycibe Roxb. and Cardiochlamyeae. In this study, we explore a large dataset of nuclear genes generated using Angiosperms353 kit, as a contribution to resolving some of these remaining phylogenetic uncertainties within Convolvulaceae. For the first time, a strongly supported backbone of the family is provided. Cuscuta is confirmed to belong within family Convolvulaceae. “Merremieae,” in their former tribal circumscription, are recovered as non-monophyletic, with the unexpected placement of Distimake Raf. as sister to the clade that contains Ipomoeeae and Decalobanthus Ooststr., and Convolvuleae nested within the remaining “Merremieae.” The monophyly of Dicranostyloideae, including Jacquemontia Choisy, is strongly supported, albeit novel relationships between genera are hypothesized, challenging the current tribal delimitation. The exact placements of Erycibe and Cuscuta remain uncertain, requiring further investigation. Our study explores the benefits and limitations of increasing sequence data in resolving higher-level relationships within Convolvulaceae, and highlights the need for expanded taxonomic sampling, to facilitate a much-needed revised classification of the family.

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Section: Methodsmentioning

confidence: 99%

A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

Simões

Eserman²,

Zuntini

et al. 2022

Front. Plant Sci.

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“…For the enriched data, the mean number of reads produced per specimen was 26,908,832 (+/-22,152,659), of which 509,242 (+/-421,822) reads mapped to the updated 353 loci target file (McLay et al, 2021). The highest number of raw and mapped reads was generated for Ccalisaya67 collected in 1838 in South America.…”

Section: Resultsmentioning

confidence: 99%

Museomic approaches to genotype historicCinchonabarks

Canales

Gardner

Gress

et al. 2022

Preprint

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Over the last few centuries, millions of plant specimens have been collected and stored within herbaria and biocultural collections. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and it is therefore increasingly difficult to characterise their genetic signatures. Here, we genotyped highly degraded Cinchona barks and leaves from herbaria using two separate high-throughput sequencing methods (HtS) and compared their performance. We subsequently genotyped specimens using genome skimming, the most commonly performed high-throughput sequencing (HtS) technique. We additionally used a recently developed capture bait set (Angiosperm353) for a target enrichment approach. Specifically, phylogenomic analyses of modern leaf and historical barks of Cinchona were performed, including 23 historical barks and six fresh leaf specimens. We found that samples degraded over time, which directly reduced the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we found that both approaches generated enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. However, the target capture kit produced data for target nuclear loci and also chloroplast data, which allowed for phylogenies to be inferred from both genomes, whereas it was only possible to use chloroplast data using genome skimming. We therefore find the Angiosperms353 target capture kit a powerful alternative to genome skimming, which can be used to obtain more information from herbarium specimens, and ultimately additional cultural benefits.

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“…However, the pattern on our A353 results could be a product of including only one reference sequence per locus [ 53 ]. This outcome could be potentially improved using the mega353 pipeline [ 54 ], as this pipeline uses more reference sequences per target to call the loci [ 55 ]. Nevertheless, our results are a strong foundation for future applications (similar to [ 21 ]) of the Angiosperms353 probe set focused on such a diverse group, such as Cactaceae.…”

Section: Discussionmentioning

confidence: 99%

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Acha

Majure

2022

Genes

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Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

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New targets acquired: Improving locus recovery from the Angiosperms353 probe set

Cited by 51 publications

References 47 publications

A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

Museomic approaches to genotype historicCinchonabarks

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

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