eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

Yu, Dalang; Dong, Lili; Yan, Fangqi; Mu, Haibo; Tang, Bixia; Yang, Xiao; Zeng, Tao; Zhou, Qing; Gao, Feng; Wang, Zhonghuang; Hao, Ziqian; Kang, Hongen; Zheng, Yi; Huang, Hongwei; Wei, Yi‐Ming; Pan, Wei; Xu, Yaochen; Zhu, Junwei; Zhao, Shilei; Wang, Ciran; Wang, Pengyu; Dai, Lina; Li, Mushan; Li, Lan; Wang, Yiwei; Chen, Hua; Li, Yixue; Fu, Yunxin; Shao, Zongshu; Bào, Yīmíng; Zhao, Fangqing; Chen, Luonan; Zhang, Guoqing; Zhao, Wenming; Li, Haipeng

doi:10.1093/nsr/nwz079

Cited by 29 publications

(23 citation statements)

References 10 publications

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“…The maximum false discovery rate of the pathway was <5% when the P-value threshold was <0.05. Proteins related to survival or metabolism were selected based on GO annotation and heatmaps 74 (Fig. 3, Supplementary Data 3 and 4).…”

Section: Methodsmentioning

confidence: 99%

Co-activation of Akt, Nrf2, and NF-κB signals under UPRER in torpid Myotis ricketti bats for survival

Huang

Liao²,

Han

et al. 2020

Commun Biol

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Bats hibernate to survive stressful conditions. Examination of whole cell and mitochondrial proteomes of the liver of Myotis ricketti revealed that torpid bats had endoplasmic reticulum unfolded protein response (UPRER), global reduction in glycolysis, enhancement of lipolysis, and selective amino acid metabolism. Compared to active bats, torpid bats had higher amounts of phosphorylated serine/threonine kinase (p-Akt) and UPRER markers such as PKR-like endoplasmic reticulum kinase (PERK) and activating transcription factor 4 (ATF4). Torpid bats also had lower amounts of the complex of Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) (p65)/I-κBα. Cellular redistribution of 78 kDa glucose-regulated protein (GRP78) and reduced binding between PERK and GRP78 were also seen in torpid bats. Evidence of such was not observed in fasted, cold-treated, or normal mice. These data indicated that bats activate Akt, Nrf2, and NF-κB via the PERK-ATF4 regulatory axis against endoplasmic reticulum stresses during hibernation.

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Section: Methodsmentioning

confidence: 99%

Co-activation of Akt, Nrf2, and NF-κB signals under UPRER in torpid Myotis ricketti bats for survival

Huang

Liao²,

Han

et al. 2020

Commun Biol

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“…To build genome tree based on autosomal SNPs datasets, we first converted VCF files to FASTA files and then constructed a neighbor-joining (NJ) tree using MEGA X [87] with the Kimura's two parameter model. To validate the converting process, we also built the genome NJ tree from the VCF file using the eGPS software [88] with the same substitution model. We also constructed a maximum likelihood (ML) tree [93].…”

Section: Phylogenetic Tree Reconstruction Based On Nuclear Genomesmentioning

confidence: 99%

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Hao

Frantz

et al. 2020

National Science Review

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110

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Pangolins are among the most critically endangered animals due to heavy poaching and world wild trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load.Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diet. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.

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“…S1a). The topology of the tree is the same as the neighbor-joining phylogenetic tree 24 from whole-genome sequences of 16 amniotes, constructed with the eGPS software 25 ( Supplementary information, Fig. S1b).…”

Section: Genome-wide Screening For Passmentioning

confidence: 99%

“…Neighbor-joining tree To visualize the accelerated evolution of PAS1, the unrooted Neighbor-Joining tree 24 of the conjunction of the accelerated cluster 1 and 2 was constructed by the eGPS software. 25 The evolutionary distances were computed using the Tajima-Nei method 72 and are in the units of the number of base substitutions per site. All positions containing gaps and missing data were eliminated.…”

Section: Detection Of Accelerated Sequences By the Kung-fu Panda (Kfpmentioning

confidence: 99%

“…To confirm the tree topology (Fig. 1a), the eGPS software 25 was used to construct another phylogenetic tree from the multigenome alignments by the Neighbor-Joining method. 24 The genetic distance was calculated by measuring the number of nucleotide substitutions, and the Kimura 2-parameter model was used to correct for multiple hits.…”

Section: Detection Of Accelerated Sequences By the Kung-fu Panda (Kfpmentioning

confidence: 99%

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Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies

Wang

Dai

et al. 2020

Cell Res

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Social hierarchies emerged during evolution, and social rank influences behavior and health of individuals. However, the evolutionary mechanisms of social hierarchy are still unknown in amniotes. Here we developed a new method and performed a genome-wide screening for identifying regions with accelerated evolution in the ancestral lineage of placental mammals, where mammalian social hierarchies might have initially evolved. Then functional analyses were conducted for the most accelerated region designated as placental-accelerated sequence 1 (PAS1, P = 3.15 × 10 −18). Multiple pieces of evidence show that PAS1 is an enhancer of the transcription factor gene Lhx2 involved in brain development. PAS1s isolated from various amniotes showed different cis-regulatory activity in vitro, and affected the expression of Lhx2 differently in the nervous system of mouse embryos. PAS1 knockout mice lack social stratification. PAS1 knock-in mouse models demonstrate that PAS1s determine the social dominance and subordinate of adult mice, and that social ranks could even be turned over by mutated PAS1. All homozygous mutant mice had normal huddled sleeping behavior, motor coordination and strength. Therefore, PAS1-Lhx2 modulates social hierarchies and is essential for establishing social stratification in amniotes, and positive Darwinian selection on PAS1 plays pivotal roles in the occurrence of mammalian social hierarchies.

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eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

Cited by 29 publications

References 10 publications

Co-activation of Akt, Nrf2, and NF-κB signals under UPRER in torpid Myotis ricketti bats for survival

Co-activation of Akt, Nrf2, and NF-κB signals under UPRER in torpid Myotis ricketti bats for survival

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies

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