A Boat Load of Genomes -- Saving Species Sequences

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An excellent overview of why and how whole genome sequencing projects are moving to record as many species genomes as possible is now available for free at LabAnimal, a Nature research journal covering in vivo studies. It provides excellent coverage of technical advances and approaches making these efforts possible and one of the cutting edge campaigns, the Vertebrate Genome Project, while still remaining clear and accessible for the average reader. Enjoy!

Micheal Eisenstein (2019) Building an Annotated Arc. LabAnimal

“Rapid evolution in hardware and software for DNA analysis and falling costs per experiment are making it easier for scientists to prospect the genomes of classic model organisms as well as novel species that intrigue them. Some groups are using this approach to explore biomedical questions in species with characteristics that parallel human traits, as seen with studies of cancer and behavioral disorders in domesticated dogs or vocal communication in songbirds. Others are studying species with unusual features that might nevertheless prove beneficial to human health, such as long-lived but cancer- and virus-resistant bats or the highly regenerative axolotl.”

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Getting Genome Annotation Right: A Refreshing Criticism

Next-generation genome annotation: we still struggle to get it right

by Steven L. Salzberg, Genome Biology, 2019

Abstract

While the genome sequencing revolution has led to the sequencing and assembly of many thousands of new genomes, genome annotation still uses very nearly the same technology that we have used for the past two decades. The sheer number of genomes necessitates the use of fully automated procedures for annotation, but errors in annotation are just as prevalent as they were in the past, if not more so. How are we to solve this growing problem?

BGI strikes back at Illumina in tit-for-tat patent infringement battle

A subsidiary of the Chinese sequencing giant BGI is filing a patent infringement suit agains the US sequencing giant. The BGI subsidiary, Complete Genomics, filed its complaint in the the District Court of Deleware, claiming infringement on a patent for “methods and compositions for efficient base calling in sequencing reactions,” which is all pretty central to high throughput sequencing. This appears to be a response to Illumina filing a complaint earlier this month against BGI Europe and Latvia MGI Tech, another BGI subsidiaries, earlier this year. These are probably just the early stages of what is likely to be a long series of antagonistic maneuvers between giants. It is unlikely that this Coke-versus-Pepsi style competition will do much to reduce the dominance of these groups, but one can hope that as this battle plays out some of the smaller sequencing players will grow and insert a little more competition into the market.

All the links in this post are from Genome-Web, another excellent genome news source.

Jumping genes are the exciting part of the Poison Frog Genome

The genome of the strawberry poison frog, Oophaga pumilio, has just been sequenced and the results show that it hosts a wide array of transposable elements, “jumping genes,” virus-like, repetitive sequences that copy themselves inside of genomes. The poison frog has a genome that is twice the size of the human genome, and two-thirds of it is composed of transposable elements. In addition, there is evidence that many of these transposable elements have recently horizontally transferred into the genome.

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog

Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G2, & Nielsen R

Abstract—We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.

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Thank you for reading!

Genome of Extreme-Tolerant Fungus from Portugal Church Sequenced

High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916

João Trovão, Igor Tiago, Fabiana Soares, Diana Sofia Paiva, Nuno Mesquita, Catarina Coelho, Lídia Catarino, Francisco Gil, and António Portugal

Christina Cuomo, Microbiology Resource Announcements

ABSTRACT—Aeminium ludgeri is an extremotolerant microcolonial black fungus isolated from a biodeteriorated limestone art piece in the Old Cathedral of Coimbra, Portugal (a UNESCO World Heritage Site). The high-quality draft genome sequence of Aeminium ludgeri presented here represents the first sequenced genome for both the recently described fungal family Aeminiaceae and the genus Aeminium.

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A high-quality raspberry genome assembly is on its way

BerryWorld Plus wins KeyGene’s genome-for-free contest

KeyGene is pleased to announce that BerryWorld Plus has won the genome-for-free contest, organised on the occasion of the Genome Insights meetup on 21 March 2019 in Wageningen. The raspberry breeders at BerryWorld Plus will receive a high-quality genome assembly of a genotype of their choice.  BerryWorld Plus was selected because they are a leader in considering state-of-the-art technology to accelerate the development of premium, healthy raspberries. With this high-quality genomic resource, raspberry breeding can now fully benefit from KeyGene’s ample experience and state of the art technologies.

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