No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects

Danchin, Antoine; Ouzounis, Christos A.; Tokuyasu, Taku A.; Zucker, Jean-Daniel

doi:10.1111/1751-7915.13284

Cited by 56 publications

(57 citation statements)

References 163 publications

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“…How could we access them? A short history of the concept will help us try and retrieve information-specific genes, while carefully browsing genome annotations (Danchin et al, 2018). Back in 1961, Rolf Landauer established that, contrary to popular belief, computation is reversible.…”

Section: Making Information a Physical Currencymentioning

confidence: 99%

Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

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Summary The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information‐managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy‐efficient way that is vastly better than our contemporary computers.

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Section: Making Information a Physical Currencymentioning

confidence: 99%

Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

Self Cite

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“…Another weakness of commonly used homology-based annota on pipelines is that they a empt to align an en re protein or mRNA sequence with a genomic sequence, a prac ce that is very likely to miss alterna ve splicing variants or pseudogenes, informa on concerning which is crucial in evolu onary studies (Danchin et al 2018;Zhang et al 2018) . In addi on, these pipelines have trouble annota ng tandem-array duplica ons, especially when there's high similarity between the copies (Zallot et al 2016;Nobre et al 2016) .…”

Section: New Approachmentioning

confidence: 99%

Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

Koludarov

Suranse³

et al. 2019

Preprint

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Gene duplica on is associated with the evolu on of many novel biological func ons at the molecular level. The dominant view, o en referred to as "neofunc onaliza on", is that duplica ons precede many novel gene func ons by crea ng func onally redundant copies which are less constrained than singletons. Numerous alterna ve models have been formulated, however, including several (such as "subfunc onaliza on" and "escape from adap ve constraints") in which novel func ons emerge prior to duplica on. Unfortunately, few studies have reconstructed the evolu onary history of a func onally diverse gene family sufficiently well to differen ate between these models. In order to understand how gene families evolve and to what extent they fit par cular evolu onary models, here we examined the evolu on of the g2 family of phospholipase A2 in 92 genomes from all major lineages of Vertebrata. This family is evolu onarily important and has been co-opted for a diverse range of func ons, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplica on events over hundreds of millions of years of evolu onary history using a novel method to annotate gene clusters, which overcomes many limita ons of automa c annota on. Surprisingly, we found that even at this level of resolu on our data could not be unambiguously fit to exis ng models of gene family evolu on. This suggests that each model may describe a part-truth that doesn't capture the full complexity of gene family evolu on. Graphical abstract Introduc onPerhaps the most important goal in evolu onary biology remains the explana on of the origins of novelty -how do new func ons, traits, and ul mately organisms arise? Gene duplica on is widely considered one of the most important mechanisms facilita ng the evolu on of novel func ons (Ohno 1970;Innan and Kondrashov 2010) . However, duplica on itself is o en treated as a "black box" -a form of "random" muta on -and numerous apparently contradictory models have been ar culated to explain the fates of duplicate genes (Conant and Wolfe 2008;Innan and Kondrashov 2010) . Although discussion of duplica on and redundancy arguably goes back to Darwin (who had no knowledge of genes and spoke of redundant "organs") and has a rich history in the 20th Century (Taylor and Raes 2004) , the "neofunc onaliza on" model of Susumu Ohno has loomed large in the field of molecular evolu on since the publica on of the seminal text "Evolu on by Gene Duplica on" in 1970 (Ohno 1970) . Briefly, this model describes gene duplica on (a neutral process) facilita ng the genesis of novelty by crea ng func onally redundant gene copies which, no longer constrained by the func onal role of the molecule encoded by the "parent" gene, enjoy a period of relaxed selec on in which neutral muta ons may accumulate. Any poten ally beneficial muta ons acquired during this period of neutral change may then be fixed by posi ve selec on.

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“…This exploration will keep going, but will begin to shift, for good, from simple correlation studies to the identification of true causal relationships. Identifying authentic causes will be successful provided we can escape the malediction of the “wisdom of the crowd” (Danchin et al ., ). With progressively more events connected to climate global change, corals will keep being in the limelight, and we can expect that their symbiotic microbiota will reveal unexpected metabolic features.…”

Section: New Concepts In Symbiosis and Evolutionmentioning

confidence: 97%