The recent rise in speed and efficiency of new sequencing technologies have
facilitated high-throughput sequencing, assembly and analyses of genomes, advancing
ongoing efforts to analyze genetic sequences across major vertebrate groups.
Standardized procedures in acquiring high quality DNA and RNA and establishing cell
lines from target species will facilitate these initiatives. We provide a legal and
methodological guide according to four standards of acquiring and storing tissue for
the Genome 10K Project and similar initiatives as follows: four-star (banked
tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and
sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual);
three-star (RNA as above and frozen tissue for 1 mg of DNA);
two-star (frozen tissue for at least 700 μg of DNA); and
one-star (ethanol-preserved tissue for 700 μg of DNA or less of
mixed quality). At a minimum, all tissues collected for the Genome 10K and other
genomic projects should consider each species’ natural history and follow
institutional and legal requirements. Associated documentation should detail as much
information as possible about provenance to ensure representative sampling and
subsequent sequencing. Hopefully, the procedures outlined here will not only
encourage success in the Genome 10K Project but also inspire the adaptation of
standards by other genomic projects, including those involving other biota.
Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
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