Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

Han, Mira V.; Thomas, Gregg W.C.; Lugo-Martinez, Jose; Hahn, Matthew W.

doi:10.1093/molbev/mst100

Cited by 698 publications

(692 citation statements)

References 40 publications

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“…The Pfam domain counts in B. platifrons were compared against the background average domain counts of the 9 non-mussel mollusks (that is, species other than B. platifrons and M. philippinarum). In addition, OrthoMCL 39 was applied to cluster gene families and CAFÉ version 3.1 was applied to determine the significance of gene family expansion/contraction 47 . For each gene family, CAFÉ generated a family-wide P value, with a significant P value indicating a possible gene-family expansion or contraction event.…”

Section: Phylogenomics Protein Sequences Of the Nine Published Or Pumentioning

confidence: 99%

“…A family-wide P value less than 0.01 and a branch/node Viterbi P value less than 0.001 was considered as a signature of gene family expansion/contraction for a specific gene family and specific species, respectively, as recommended for CAFÉ version 3.1 in ref. 47 . Proteomics characterization.…”

Section: Phylogenomics Protein Sequences Of the Nine Published Or Pumentioning

confidence: 99%

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Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

et al. 2017

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Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

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Section: Phylogenomics Protein Sequences Of the Nine Published Or Pumentioning

confidence: 99%

Section: Phylogenomics Protein Sequences Of the Nine Published Or Pumentioning

confidence: 99%

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

et al. 2017

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“…Another important requirement for this approach is the quality of sequencing and annotation, especially for a large gene family, as sequencing errors and misannotations can lead to false positives when testing for positive selection (Han et al, 2013). We profit from a recently developed pipeline designed to automatically perform different steps of the analysis (Fischer et al, 2014).…”

Section: Studying Selection Pressures In a Large And Dynamic Gene Familymentioning

confidence: 99%

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

et al. 2016

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Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a d N /d S -based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.

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“…Supplemental Table S20 summarizes the number of reads, mapping percentage, and coverage prior to and after removing PCR duplicates. Assessment of canonical pathway enrichment for genes linked with deleted or duplicated bases utilized a hypergeometric test (P < 0.05) against the human genome enabled in WebGestalt (Wang et al 2013), while examination of gene family expansion and contraction used the updated CAFE3 (see Supplemental Methods; Han et al 2013). …”

Section: Structural Variation Detectionmentioning

confidence: 99%

The genome of the vervet (Chlorocebus aethiops sabaeus)

et al. 2015

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We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.

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Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

Cited by 698 publications

References 40 publications

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

The genome of the vervet (Chlorocebus aethiops sabaeus)

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