Population structure and adaptability analysis of Schizothorax o’connori based on whole-genome resequencing DOI Creative Commons

Kuo Gao,

Zhi He,

Jinxin Xiong

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 6, 2024

Abstract Background Schizothorax o’connori is an endemic fish distributed in the upper and lower reaches of Yarlung Zangbo River China. It has experienced a fourth round whole gene replication events good model for exploring genetic differentiation environmental adaptability Qinghai-Tibet Plateau. The uplift Plateau led to changes river system, thereby affecting exchange population between populations. With release genome data, resequencing been widely used evolutionary analysis screening selected genes fish, which can better elucidate basis molecular adaptation mechanisms fish. Therefore, our purpose this study was understand structure adaptive characteristics S. using whole-genome method . Results results showed that 23,602,746 SNPs were identified from seven populations, mostly on chromosomes 2 23. There no significant diversity relatively low. However, Zangga could be separated Bomi, Linzhi, Milin populations cluster analysis. Based historical dynamics population, size ancestral affected by late accelerated Qinghai Tibet Fourth Glacial Age. sites enriched pathways related DNA repair energy metabolism. Conclusion Overall, provides valuable insights into obvious at level upstream downstream River. current distribution pattern are influenced Ice metabolism adapt low temperature strong ultraviolet radiation environment high altitude.

Language: Английский

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads DOI Creative Commons
Jiang Hu, Zhuo Wang, Zongyi Sun

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 26, 2024

Long-read sequencing data, particularly those derived from the Oxford Nanopore platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient correction and assembly tool for noisy long reads, which achieves a level of accuracy in genome assembly. We apply NextDenovo assemble 35 diverse human genomes around world using long-read data. These allow us identify landscape segmental duplication gene copy number variation modern populations. The use should pave way population-scale

Language: Английский

Citations

159
An efficient error correction and accurate assembly tool for noisy long reads DOI Creative Commons
Jiang Hu, Zhuo Wang, Zongyi Sun

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 12, 2023

Abstract Long read sequencing data, particularly those derived from the Oxford Nanopore (ONT) platform, tend to exhibit a high error rate. Here, we present NextDenovo, highly efficient correction and assembly tool for noisy long reads, which achieves level of accuracy in genome assembly. NextDenovo can rapidly correct reads; these corrected reads contain fewer errors than other comparable tools are characterized by chimeric alignments. We applied quality reference genomes 35 diverse humans across world using ONT data. Based on de novo assemblies, were able identify landscape segmental duplications gene copy number variation modern human population. The use program should pave way population-scale long-read assembly, thereby facilitating construction pan-genomes,

Language: Английский

Citations

103
The genomes of all lungfish inform on genome expansion and tetrapod evolution DOI
Manfred Schartl, Joost M. Woltering, Iker Irisarri

et al.

Nature, Journal Year: 2024, Volume and Issue: 634(8032), P. 96 - 103

Published: Aug. 14, 2024

Language: Английский

Citations

12
Recent advances in the use of antarctic krill (Euphausia superba) as a sustainable source of high-quality protein: A comprehensive review DOI

S.-K. Tang,

Jing Jing Wang, LI Yu-feng

et al.

Trends in Food Science & Technology, Journal Year: 2024, Volume and Issue: 152, P. 104684 - 104684

Published: Aug. 31, 2024

Language: Английский

Citations

10
Characterization of oxylipins in Antarctic krill oil (Euphausia superba) during storage based on RPLC–MS/MS analysis DOI
Nan Meng, Xincen Wang, Yu Song

et al.

Food Chemistry, Journal Year: 2024, Volume and Issue: 445, P. 138702 - 138702

Published: Feb. 10, 2024

Language: Английский

Citations

9
The amphipod genome reveals population dynamics and adaptations to hadal environment DOI Creative Commons
Haibin Zhang, Shuai Sun, Jun Liu

et al.

Cell, Journal Year: 2025, Volume and Issue: 188(5), P. 1378 - 1392.e18

Published: March 1, 2025

Language: Английский

Citations

1
Translating genomic advances into biodiversity conservation DOI
Carolyn J. Hogg

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(5), P. 362 - 373

Published: Nov. 27, 2023

Language: Английский

Citations

22
Climate change impacts on Antarctic krill behaviour and population dynamics DOI
So Kawaguchi, Angus Atkinson, Dominik Bahlburg

et al.

Nature Reviews Earth & Environment, Journal Year: 2023, Volume and Issue: 5(1), P. 43 - 58

Published: Dec. 19, 2023

Language: Английский

Citations

19
Dietary antarctic krill improves antioxidant capacity, immunity and reduces lipid accumulation, insights from physiological and transcriptomic analysis of Plectropomus leopardus DOI Creative Commons
Mengya Wang,

Shaoxuan Wu,

Hui Ding

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 26, 2024

Abstract Background Due to its enormous biomass, Antarctic krill ( Euphausia superba ) plays a crucial role in the Ocean ecosystem. In recent years, has found extensive application aquaculture, emerging as sustainable source of aquafeed with ideal nutritional profiles. However, comprehensive study focused on detailed effects dietary aquaculture animals, especially farmed marine fishes, is yet be demonstrated. Results this study, comparative experiment was performed using juvenile P. leopardus , fed diets supplemented (the group) or without control group). Histological observation revealed that could reduce lipid accumulation liver while intestine exhibited no obvious changes. Enzyme activity measurements demonstrated had an inhibitory effect oxidative stress both and liver. By transcriptome analysis, total 1,597 1,161 differentially expressed genes (DEGs) were identified liver, respectively. Functional analysis DEGs showed multiple enriched terms significantly related cholesterol metabolism, antioxidants, immunity. Furthermore, expression profiles representative DEGs, such dhcr7 apoa4 sc5d scarf1 validated by qRT-PCR fluorescence situ hybridization. Finally, demonstrate biased astaxanthin . Conclusions Our enhance antioxidant capacities exhibit molecular-level improvements immunity, antioxidants. It will contribute understanding protective provide insights into strategies.

Language: Английский

Citations

7
Exploring the enigma: history, present, and future of long non-coding RNAs in cancer DOI Creative Commons
Qais Ahmad Naseer,

Abdul Malik,

Fengyuan Zhang

et al.

Discover Oncology, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 7, 2024

Abstract Long noncoding RNAs (lncRNAs), which are more than 200 nucleotides in length and do not encode proteins, play crucial roles governing gene expression at both the transcriptional posttranscriptional levels. These molecules demonstrate specific patterns various tissues developmental stages, suggesting their involvement numerous processes diseases, notably cancer. Despite widespread acknowledgment growing enthusiasm surrounding potential as diagnostic prognostic biomarkers, precise mechanisms through lncRNAs function remain inadequately understood. A few have been studied depth, providing valuable insights into biological activities emerging functional themes mechanistic models. However, extent to mammalian genome is transcribed transcripts still a matter of debate. This review synthesizes our current understanding lncRNA biogenesis, genomic contexts, multifaceted tumorigenesis, highlighting cancer-targeted therapy. By exploring historical perspectives alongside recent breakthroughs, we aim illuminate diverse reflect on broader implications study for evolution function, well advancing clinical applications.

Language: Английский

Citations

7