Current methods for automated annotation of protein-coding genes

Hoff, KJ; Stanke, Mario

doi:10.1016/j.cois.2015.02.008

Cited by 25 publications

(18 citation statements)

References 51 publications

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“…To begin the annotation process, we annotated the genome exclusively with the N. vespilloides Cufflinks-assembled transcripts and the proteomes from five insects ( T. castaneum, N. vitripennis, A. mellifera, M. domestica, D. melanogaster ; downloaded from UniProtKB, including all isoforms for comprehensive coverage) using default parameters, except for est2genome=1, protein2genome=1. After this first iteration of annotation (and every subsequent iteration), three scaffolds were inspected to visually check for annotation biases (Hoff and Stanke, 2015) using Apollo genome browser (Lewis et al , 2002). The next iteration used the same input data and parameters, except changes to split_hit=2000, correct_est_fusion=1, which corrected for the smaller intron size observed and the propensity of MAKER to fuse gene models that likely should be separate as inferred by visual inspection of BLAST evidence.…”

Section: Methodsmentioning

confidence: 99%

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Cunningham

Wiberg

et al. 2015

Preprint

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22Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of 23 genomes available for comparison spanning multiple independent lineages. For example, complex social 24 behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are 25 Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa 26 that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle 27 Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social 28 behavior. We used this genome to address two questions. First, does life history predict overlap in gene 29 models more strongly than phylogenetic groupings? Second, like other insects with highly developed social 30 behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene 31 models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike 32 previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be 33 used to address questions about the potential role of methylation in social behavior. The addition of this 34 genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of 35 sociality. 36 37 Introduction 38Understanding phenotypic evolution necessitates investigating both the ultimate and proximate influences on 39 traits; however, these investigations require the appropriate tools. Social behavior is a particularly thorny 40 phenotype to study because of its complexity, variation, and its multi-level integration across an organism 41 (Boake et al., 2002). In addition, social behavior also often displays unusual evolutionary dynamics arising 42 from the genetic influences on interactions required for sociality (McGlothlin et al., 2010). Although single 43 genes can influence behavior (Fischman et al., 2011), social behavior is often multifaceted and can reflect a 44 complex genetic architecture (Walling et al., 2008; Mikheyev and Linksvayer, 2015) including influences 45 from epigenetic mechanisms (Cardoso et al., 2015). Genomes in particular are useful resources for 46 evolutionary questions of social behavior because they grant access to both broad scale and fine scale details 47 and mechanisms (Richards, 2015). For social behavior, while there are multiple Hymenopteran genomes 48 available to investigate fine scale detail, we lack sufficiently distantly related species to address broader 49 patterns. It is therefore important to develop genomic resources for organisms that are particularly 50 phenotypic models of social behavior but where genomic information is lacking. 51The genomes of several social insect are now available, including eusocial species such as honey 52 bees (Elsik et al., 2014), stingless bees (Kapheim et al., 2015), several ant species (Gadau et al., 2012), a 53 termite (Terrapon et al., 2...

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Section: Methodsmentioning

confidence: 99%

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Cunningham

Wiberg

et al. 2015

Preprint

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“…For instance, a survey from 2013 (Steijger et al, 2013) suggests that even the most accurate tools are merely predicting 48.53% of the genes (at least one splice form) in Drosophila melanogaster correctly, when using only RNA-Seq data as evidence. For a recent review on the subject, see Hoff and Stanke (2015).…”

Section: Introductionmentioning

confidence: 99%

Simultaneous gene finding in multiple genomes

König

Romoth

Gerischer

et al. 2015

Preprint

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As whole genome sequencing is taking on ever-increasing dimensions, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or -if notwhere the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on a whole-genome alignment of 12 Drosophila species and its accuracy evaluated on D. melanogaster. The method is being implemented as an extension to the gene finder AUGUSTUS.

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“…In species with sufficient transcriptome data, mapping these data to the assembly generally performs far better at gene finding than the de-novo approaches outlined above [55,56].…”

Section: Transcriptome Evidence Based Comparative Annotationmentioning

confidence: 99%

“…Annotation pipelines such as MAKER [39], RefSeq [38] and AUGUSTUS [61] make use of both approaches. See [56] for a recent review of genome annotation methods.…”

Section: Introductionmentioning

confidence: 99%

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

Fiddes

Armstrong

Diekhans

et al. 2017

Preprint

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The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of new, ultra-contiguous genome assemblies. To compare these genomes we need robust methods for genome annotation. We describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. We demonstrate the resulting discovery of novel genes, isoforms and structural variants, even in genomes as well studied as rat and the great apes, and how these annotations improve cross-species RNA expression experiments.

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Current methods for automated annotation of protein-coding genes

Cited by 25 publications

References 51 publications

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Simultaneous gene finding in multiple genomes

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

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