Abstract：
:High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked-read technology and four published genomes assembled from a single shotgun library. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof-of-concept, we used annotated genes from the four Peromyscus linked-read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked-read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Colella JP,Tigano A,MacManes MDdoi
10.1111/1755-0998.13155subject
Has Abstractpub_date
2020-07-01 00:00:00pages
856-870issue
4eissn
1755-098Xissn
1755-0998journal_volume
20pub_type
杂志文章abstract：:An enriched genomic library was constructed and 9 novel polymorphic tetranucleotide microsatellite markers developed for Austrocedrus chilensis, the most economically important native conifer in the Andean Patagonian region. Polymorphism was investigated for these markers in 48 individuals from two populations. Number...
journal_title：Molecular ecology resources
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journal_title：Molecular ecology resources
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journal_title：Molecular ecology resources
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journal_title：Molecular ecology resources
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doi：10.1111/1755-0998.13018
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pub_type： 杂志文章,评审
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journal_title：Molecular ecology resources
pub_type： 杂志文章
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pub_type： 杂志文章
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journal_title：Molecular ecology resources
pub_type： 杂志文章
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journal_title：Molecular ecology resources
pub_type： 杂志文章
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更新日期：2009-03-01 00:00:00
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journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12578
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pub_type： 杂志文章
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journal_title：Molecular ecology resources
pub_type： 杂志文章
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journal_title：Molecular ecology resources
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