Opportunities and challenges for high‐quality biodiversity tissue archives in the age of long‐read sequencing

Blom, Mozes P. K.

doi:10.1111/mec.15909

Cited by 28 publications

(33 citation statements)

References 151 publications

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“…Samples are currently in the process of being collected by incountry scientists and experts who are in charge of sampling and archiving specific types of metadata for each specimen. Without such data, type specimens and previous data collections cannot be ground-truthed or revised (Blom, 2021;Buckner et al, 2021), which ultimately limits the usefulness of -omics data for current and future analyses. One additional barrier is the lack of a central repository that integrates (i) several or all types of data (genomic, taxonomic, physiological, chemico-physical, etc.)…”

Section: Discussion and Perspectivementioning

confidence: 99%

“…highly divergent (LaJeunesse et al, 2005;Lin, 2011;Aranda et al, 2016;González-Pech et al, 2019, 2021Nand et al, 2021; Supplementary Table 4). Initially, all Symbiodiniaceae were thought to comprise a single species (Freudenthal, 1962;Kevin et al, 1969;Taylor, 1974), but the accumulation of molecular data has led to our current understanding that there are likely hundreds of species spread across tens of genera within this microalgal family (LaJeunesse et al, 2018).…”

Section: The Microalgal Symbiont (Symbiodiniaceae)mentioning

confidence: 99%

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Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

et al. 2021

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Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.

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Section: Discussion and Perspectivementioning

confidence: 99%

Section: The Microalgal Symbiont (Symbiodiniaceae)mentioning

confidence: 99%

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

et al. 2021

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“…The approaches from Helicos and Oxford allow direct sequencing of DNA or RNA. Additionally, long-read sequencing platforms have great potential in many research areas [5,6], allowing annotations without, or with lower, assembly requirements (depending on the source sequence length), streamlining data processing workflows [7]. In particular, Pacific Biosciences generates long reads of 20 kb on average, reaching 300 kb [8].…”

Section: Three Sequencing Generationsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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“…Yamaguchi et al (2021) discuss the role of Hi-C data in allowing chromosome scale genome assemblies to be widely available in non-model organisms without available linkage maps, and present a detailed description of the Hi-C method and provide important technical considerations. Blom (2021) addresses the increasing availability and advantages of long-read sequencing within the field of molecular ecology, and the potential of reference-free assemblies for multiple individuals of a species for a better representation of the full genetic variation within and between populations. A major focus of this review, however, is on the urgent need to collect and preserve high-quality samples given drastic global biodiversity declines.…”

Section: Me Thodolog Ic Al Approache S and Advan Ce S For Wg Smentioning

confidence: 99%

Seeing the whole picture: What molecular ecology is gaining from whole genomes

et al. 2021

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Opportunities and challenges for high‐quality biodiversity tissue archives in the age of long‐read sequencing

Cited by 28 publications

References 151 publications

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Seeing the whole picture: What molecular ecology is gaining from whole genomes

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