Genetic variation in PTPN1 contributes to metabolic adaptation to high-altitude hypoxia in Tibetan migratory locusts

Animal and human highlanders have evolved distinct traits to enhance tissue oxygen delivery and utilization. Unlike vertebrates, insects use their tracheal system for efficient oxygen delivery. However, the genetic basis of insect adaptation to high-altitude hypoxia remains unexplored. Here, we report a potential mechanism of metabolic adaptation of migratory locusts in the Tibetan Plateau, through whole-genome resequencing and functional investigation. A genome-wide scan revealed that the positively selected genes in Tibetan locusts are predominantly involved in carbon and energy metabolism. We observed a notable signal of natural selection in the gene PTPN1, which encodes PTP1B, an inhibitor of insulin signaling pathway. We show that a PTPN1 coding mutation regulates the metabolism of Tibetan locusts by mediating insulin signaling activity in response to hypoxia. Overall, our findings provide evidence for the high-altitude hypoxia adaptation of insects at the genomic level and explore a potential regulatory mechanism underlying the evolved metabolic homeostasis.

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A description of all covariates tested A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons A full description of the statistics including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals) For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted

Software and code
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Data
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Study description
In this study, we have compared the genetic differences between Tibetan and lowland locust populations and investigated the genetic mechanism of hypoxia adaptation for Tibetan locust. For genome sequencing, 12 field collected Tibetan locust samples and 10 field collected lowland locust samples were used. For functional and transcriptome study, experimental groups were treated with 10 kPa hypoxia for 120 h, and normoxia groups were used as control. For in vivo study, each experiment contains at least 4 replicates. For western blot and in vitro experiment at least 3 replicates were used. Each replicate contains three locusts.
Research sample 1) Tibetan locusts, Locusta migratoria populations that habitat in Tibetan plateau; 2) Lowland locusts, Locusta migratoria populations that habitat in South China plain. The Tibetan and South China lowland locust populations belong to same lineage around worldwide locust populations. Both male and female adult locusts were selected randomly for whole genome resequencing.

Sampling strategy
Locusts sampled at each locality were caught at more than ten sites that are spaced over 300 meters between each other. Approximately 50 locusts were collected at each site.

Data collection
For quantitative PCR, data were generated by a LightCycler 480 instrument (Roche, USA). Gene expression level was calculated via 2^-ΔCt, significance level was analyzed by Student's t-test. For metabolite measurement, trehalose and glucose was tested by Agilent 6890N-5973N, the data were generated by software AMDIS. For Colorimetric/Fluorometric Assay, data were generated via a multi-mode detection platform (Paradigm, USA) and analysed with software GraphPad Prism 5. For micrographs, photos were captured by LSM 710 confocal fluorescence microscope (Zeiss, Germany). At least five tissue sections (five individuals) from each treatment were used for data analysis. For lifespan assay, 30 locusts was used in each group. Death events was calculated twice a day. The final data was analysed with software SPSS. Data were collected by Ding Ding.
Timing and spatial scale For whole genome re-sequencing, locust samples from Maizhikungga were collected in 2005, locust samples from Lhasa were collected in 2014, Two samples from Shanan and Doilong were collected in 2015, another sample from Doilong was collected in 2005 and samples from lowland were collected in 2014. For functional study, Tibetan locust samples were collected from Lhasa in 2014, 2015 and 2016.

Data exclusions
No data was excluded.

Reproducibility
In the current study, quantitative experiments were performed with at least three biological samples. Some important assays were repeated for 3 times for each sample. All attempts to repeat the experiment were successful.

Randomization
Samples for assay were randomly allocated.

Blinding
Blinding was used for all data acquisition and analysis.
Did the study involve field work?

Animals and other organisms
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Laboratory animals
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Wild animals
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Field-collected samples
Field-collected locusts were maintained in the laboratory at the Institute of Zoology, Chinese Academy of Sciences in Beijing (<50