Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

@article{Zhang2013ComparativeAO,
  title={Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity},
  author={Guojie Zhang and Christopher J Cowled and Zh{\`e}ngl{\`i} Sh{\'i} and Zhiyong Huang and Kimberly A. Bishop-Lilly and Xiaodong Fang and James W. Wynne and Zhiqiang Xiong and Michelle L. Baker and Wei Zhao and Mary Tachedjian and Yabing Zhu and Peng Zhou and Xuanting Jiang and Justin Han Jia Ng and Lan Yang and Lijun Wu and Jin Xiao and Yue Feng and Yuanxin Chen and Xiaoqing Sun and Yong Zhang and Glenn A. Marsh and Gary S Crameri and Christopher C. Broder and Kenneth G. Frey and Lin‐Fa Wang and Jun Wang},
  journal={Science},
  year={2013},
  volume={339},
  pages={456 - 460}
}
Bat Genomes Bats are of great interest because of their ability to fly and as hosts for infectious disease. Zhang et al. (p. 456, published online 20 December) sequenced the genomes of two distantly related bat species, David's Myotis and Black flying fox. Analysis of the two genomes revealed likely changes that accompanied the evolution of bats, including selection for increased expression of genes involved in the oxidative phosphorylation pathway needed to generate the energy required for… 
Bat immunology takes off
TLDR
It is suggested that flight-associated adaptations inadvertently shaped the bat immune system and led to the selection of genes that promote damage sensing and repair, many of which also contribute to antiviral immunity.
Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems. To investigate the genomic underpinnings of unique bat adaptations, we sequenced the
BGD: A Database of Bat Genomes
TLDR
The Bat Genome Database (BGD) is an open-access, web-available portal that integrates available data of bat genomes and genes and will extend the understanding of the bat evolution and be advantageous to the bat sequences analysis.
Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing
TLDR
Characterisation of the bat microRNA repertoire is an essential step towards understanding transcriptional regulation during viral infection, and will assist in the identification of mechanisms that enable bats to act as natural virus reservoirs, which will facilitate the development of antiviral strategies for use in humans and other species.
Comparative genomics reveals contraction in olfactory receptor genes in bats
TLDR
Comparative evolutionary analyses of complete proteome data for eight bat species, including echolocating and non-echolocating forms, together with the proteomes of 12 other laurasiatherian mammals revealed extensive gene loss in the most recent ancestor of bats, and also of carnivores, although this gene contraction did not appear to correlate with the reduction in genome size in bats.
Evolution and comparative analysis of the bat MHC-I region
TLDR
It is hypothesised that MHC-I genes first originated in the β duplication block, and subsequently duplicated in a step-wise manner across the M HC-I region during mammalian evolution.
Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus
TLDR
Signs of rapid evolution in the innate immune response genes of bats, and evidence of past infections with diverse viral clades in Artibeus jamaicensis and Pteronotus mesoamericanus are found.
Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.
TLDR
The unique adaptations of bats are reviewed and how chromosome-level genome assemblies can uncover the molecular basis of these traits are highlighted to better understand, promote, and conserve bats.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 51 REFERENCES
The immune gene repertoire of an important viral reservoir, the Australian black flying fox
TLDR
This study describes the immune transcriptome of the Australian flying fox, Pteropus alecto, providing an important resource for identification of genes involved in a range of activities including antiviral immunity, and provides a survey of expressed bat genes that complement existing bat genomic data.
Adaptive evolution of energy metabolism genes and the origin of flight in bats
TLDR
Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting the hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.
Endogenous Viral Elements in Animal Genomes
TLDR
It is established that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.
Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus
TLDR
Evidence for the colonization of a mammalian genome by Helitrons is provided and an instance of HeliBat-mediated transduction of a host gene fragment that was subsequently dispersed in ≈1,000 copies throughout the M. lucifugus genome is described.
Estimating the tempo and mode of gene family evolution from comparative genomic data.
TLDR
A model of stochastic birth and death for gene family evolution is used and it is shown that it can be efficiently applied to multispecies genome comparisons and offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection.
The mammalian PYHIN gene family: Phylogeny, evolution and expression
TLDR
It is hypothesised that defence of the genome against endogenous retroelements has been an additional evolutionary driver for PYHIN proteins.
The genome sizes of megabats (Chiroptera: Pteropodidae) are remarkably constrained
TLDR
The present study provides genome size estimates for 43 species of megabats in an effort to fill the gap and to test the hypothesis that all bats, and not just microbats, possess small genomes.
PAML 4: phylogenetic analysis by maximum likelihood.
TLDR
PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
...
1
2
3
4
5
...