Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild DOI Creative Commons
Yisi Hu, Yibo Hu, Wenliang Zhou

et al.

Annual Review of Animal Biosciences, Journal Year: 2023, Volume and Issue: 12(1), P. 69 - 89

Published: Oct. 20, 2023

Giant pandas and red are endangered species with similar specialized bamboo diet partial sympatric distribution in China. Over the last two decades, rapid development of genomics metagenomics research on these has enriched our knowledge their biology, ecology, physiology, genetics, evolution, which is crucial useful for conservation. We describe evolutionary history, endangerment processes, genetic diversity, population structure wild giant (Chinese Himalayan pandas). In addition, we explore how studies have provided insight into convergent adaptation to diet. Finally, discuss findings applied effective conservation management captivity promote long-term persistence species.

Language: Английский

Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryotes DOI
Weibo Zheng, Chao Li,

Zhaorui Zhou

et al.

Science China Life Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

Citations

2
Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards DOI Creative Commons
Lin Yang, Hongjian Jin, Qi‐En Yang

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 14, 2025

Long-term persistence of species with low genetic diversity is the focus widespread attention in conservation biology. The snow leopard, Panthera uncia, a big cat from high-alpine regions Asia. However, its subspecies taxonomy, evolutionary history, potential, and survival strategy remain unclear, which greatly hampers their conservation. We sequence high-quality chromosome-level genome leopard genomes 52 wild leopards. Population genomics reveal existence two large lineages global leopards, northern southern lineages, supported by biogeography. Last Glacial Maximum drove divergence lineages. Microclimate differences rivers between western central Himalayas likely maintain differentiation EPAS1 positively selected lineage almost fixed amino acid substitutions shows an increased allele frequency elevation. Compared to lineage, exhibits lower level genomic higher levels inbreeding load, consistent recent population decline. find that leopards have extremely than other Carnivora species; however, strong deleterious mutations been effectively purged historical bottlenecks inbreeding, may be vital mechanism for viability. Our findings highlight importance unveiling both burden threatened species.

Language: Английский

Citations

1
A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice DOI Creative Commons

Xiaofeng Zu,

Lilan Luo, Zhen Wang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 25, 2023

Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations impair intron splicing nad4 nad5 transcripts decrease RNA editing efficiency nad2, nad6, rps4 transcripts, resulting deficiencies mitochondrial complex I, thus ROS generation rescuing phenotype. Overexpression different compartment-localized superoxide dismutases (SOD) genes reverses over-accumulation phenotypes various degrees, with Mn-SOD reversing best. Mutation indica varieties enhances cold tolerance lower levels. We find that plays key role responses, identify modulating factor, informing efforts improve tolerance.

Language: Английский

Citations

21
Transcriptome Expression Profiling Reveals the Molecular Response to Salt Stress in Gossypium anomalum Seedlings DOI Creative Commons
Huan Yu, Qi Guo,

Wei Ji

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(2), P. 312 - 312

Published: Jan. 20, 2024

Some wild cotton species are remarkably tolerant to salt stress, and hence represent valuable resources for improving tolerance of the domesticated allotetraploid Gossypium hirsutum L. Here, we first detected salt-induced stress changes in physiological biochemical indexes G. anomalum, a African diploid species. Under 350 mmol/L NaCl treatment, photosynthetic parameters declined significantly, whereas hydrogen peroxide (H2O2) malondialdehyde (MDA) contents increased. Catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) activity proline (PRO) content also significantly increased, reaching peak values at different stages stress. We used RNA-Seq characterize 15,476 differentially expressed genes anomalum roots after 6, 12, 24, 72, 144 h Gene Ontology enrichment analysis revealed these be related sequence-specific DNA iron ion binding oxidoreductase, peroxidase, antioxidant, transferase activity; meanwhile, top enriched pathways from Kyoto Encyclopedia Genes Genomes database were plant hormone signal transduction, phenylpropanoid biosynthesis, fatty acid degradation, carotenoid zeatin starch sucrose metabolism, MAPK signaling. A total 1231 transcription factors found response representing ERF, MYB, WRKY, NAC, C2H2, bZIP, HD-ZIP families. Nine candidate validated by quantitative real-time PCR their expression patterns consistent with data. These data promise advance our understanding molecular spp., potential value breeding applications.

Language: Английский

Citations

6
Gut microbiome as a key monitoring indicator for reintroductions of captive animals DOI Open Access
Guangping Huang,

Dunwu Qi,

Zhisong Yang

et al.

Conservation Biology, Journal Year: 2023, Volume and Issue: 38(1)

Published: Aug. 31, 2023

Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years characterize ecological succession adaptive evolution captive giant pandas reintroduced wild. We collected 63 fecal samples from 3 individuals 22 9 wild 96 publicly available another individuals. By microbial composition analysis, identified community clusters microbiome (here termed enterotypes) with interenterotype was closely related process. Each enterotypes based on significant variation in levels 1 genera: Clostridium, Pseudomonas, Escherichia. The enterotype This gradually replaced by Clostridium during wild-training process, which turn Pseudomonas resembled pandas, conversion wildness a successful reintroduction. also isolated strain protegens enterotype, previously reported free-living microbe, found its within-host contributed host dietary adaptation Monitoring structure provides novel, noninvasive tool can individual

Language: Английский

Citations

14
Masting promotes transformation from predation to mutualism in an oak-weevil-rodent system DOI
Hongmao Zhang, Hongyu Niu, Michael A. Steele

et al.

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(7), P. 1514 - 1524

Published: March 25, 2024

Language: Английский

Citations

5
PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation DOI Creative Commons
Guangping Huang, Wenyu Shi, Le Wang

et al.

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: Oct. 7, 2023

Abstract Background The gut microbiota play important roles in host adaptation and evolution, but are understudied natural population of wild mammals. To address adaptive evolution improve conservation efforts threatened mammals from a metagenomic perspective, we established high-quality microbiome catalog the giant panda (pandaGUT) to resolve diversity, functional, resistome landscapes using approximately 7 Tbp long- short-read sequencing data 439 stool samples. Results pandaGUT comprises 820 metagenome-assembled genomes, including 40 complete closed 64.5% which belong species that have not been previously reported, greatly expanding coverage most prokaryotic lineages. contains 2.37 million unique genes, with 74.8% possessing open read frames, facilitating future mining microbial functional potential. We identified three enterotypes across captive populations characterized by Clostridium , Pseudomonas Escherichia respectively. found pandas exhibited genetic-specific structures functions, suggesting host-gut phylosymbiosis, while cohorts encoded more multi-drug resistance genes. Conclusions Our study provides largely untapped resources for biochemical biotechnological applications as well potential intervention avenues via rational manipulation diversity reducing antibiotic usage management wildlife.

Language: Английский

Citations

12
Evolutionary genomics of camouflage innovation in the orchid mantis DOI Creative Commons
Guangping Huang,

Lingyun Song,

Xin Du

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 10, 2023

Abstract The orchid mantises achieve camouflage with morphological modifications in body color and pattern, providing an interesting model for understanding phenotypic innovation. However, a reference genome is lacking the order Mantodea. To unveil mechanisms of plant-mimicking coloration patterns, we performed de novo assembly two chromosome-level genomes mantis its close relative, dead leaf mantis. Comparative genomic analysis revealed that Scarlet gene plays important role synthesis xanthommatin, pigment coloration. Combining developmental transcriptomic genetic engineering experiments, found cuticle was essential component ‘petal-like’ enlargement, specific expression ventral femur controlled by Wnt signaling. prolonged Ultrabithorax (Ubx) accompanied femoral expansion suggested Ubx determines leg remodeling early stage. We also evidence evolution Trypsin family insectivory adaptation ecdysone-dependent sexual dimorphism size. Overall, our study presents new catalogs reveals evolutionary underlying unique praying mantis, insights into innovation adaptation.

Language: Английский

Citations

11
Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown-and-white coat color in giant pandas DOI
Dengfeng Guan,

Shuyan Sun,

Lingyun Song

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(11)

Published: March 4, 2024

Brown-and-white giant pandas (hereafter brown pandas) are distinct coat color mutants found exclusively in the Qinling Mountains, Shaanxi, China. However, its genetic mechanism has remained unclear since their discovery 1985. Here, we identified basis for this variation using a combination of field ecological data, population genomic and CRISPR–Cas9 knockout mouse model. We de novo assembled long-read-based panda genome resequenced genomes 35 pandas, including two family trios associated with panda. homozygous 25-bp deletion first exon Bace2 , gene encoding amyloid precursor protein cleaving enzyme, as most likely brown-and-white color. This was further validated PCR Sanger sequencing another 192 black CRISPR-Cas9 edited mice. Our investigation revealed that mutation reduced number size melanosomes hairs mice possibly panda, leading to hypopigmentation. These findings provide unique insights into wild animals.

Language: Английский

Citations

4
Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems DOI

Suxiang Lu,

Honghui Zeng, Fan Xiong

et al.

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(7), P. 1368 - 1384

Published: March 18, 2024

Language: Английский

Citations

4