Aleksander SA, Balhoff J, Carbon S et al (2023) The Gene Ontology knowledgebase in 2023. Genetics 224. https://doi.org/10.1093/genetics/iyad031

Alexandre PA, Reverter A, Berezin RB et al (2020) Exploring the regulatory potential of long non-coding RNA in feed efficiency of indicine cattle. Genes (Basel) 11. https://doi.org/10.3390/genes11090997

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Billerey C, Boussaha M, Esquerré D et al (2014) Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 15:499. https://doi.org/10.1186/1471-2164-15-499

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cai W, Li C, Liu S et al (2018) Genome wide identification of novel long non-coding RNAs and their potential associations with milk proteins in Chinese Holstein cows. Front Genet 9:281. https://doi.org/10.3389/fgene.2018.00281

Article  CAS  PubMed  PubMed Central  Google Scholar 

Deniz E, Erman B (2017) Long noncoding RNA (lincRNA), a new paradigm in gene expression control. Funct Integr Genomics 17:135–143. https://doi.org/10.1007/s10142-016-0524-x

Article  CAS  PubMed  Google Scholar 

Deveson IW, Hardwick SA, Mercer TR, Mattick JS (2017) The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome. Trends Genet 33:464–478. https://doi.org/10.1016/j.tig.2017.04.004

Article  CAS  PubMed  Google Scholar 

Dinger ME, Amaral PP, Mercer TR et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433–1445. https://doi.org/10.1101/gr.078378.108

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dou Y, Qi K, Liu Y, Li C, Song C, Wei Y, Zhang Z, Li X, Wang K, Li X et al (2023) Identification and functional prediction of long non-coding RNA in longissimus dorsi muscle of Queshan black and large white pigs. Genes 14(1):197. https://doi.org/10.3390/genes14010197

Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/btw354

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu H, Jia Q, Xi J et al (2020) Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows. BMC Genomics 21:636. https://doi.org/10.1186/s12864-020-07055-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang Y, Shen Y, Zou H, Jiang Q (2021) Analysis of long non-coding RNAs in skeletal muscle of Bama Xiang pigs in response to heat stress. Trop Anim Health Prod 53:259. https://doi.org/10.1007/s11250-021-02701-7

Article  PubMed  Google Scholar 

Hudson WH, Ortlund EA (2014) The structure, function and evolution of proteins that bind DNA and RNA. Nat Rev Mol Cell Biol 15:749–760. https://doi.org/10.1038/nrm3884

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang N, Zhang X, Gu X et al (2021) Progress in understanding the role of lncRNA in programmed cell death. Cell Death Dis 7:30. https://doi.org/10.1038/s41420-021-00407-1

Article  CAS  Google Scholar 

Jiang S, Cheng S-J, Ren L-C et al (2019) An expanded landscape of human long noncoding RNA. Nucleic Acids Res 47:7842–7856. https://doi.org/10.1093/nar/gkz621

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kern C, Wang Y, Chitwood J et al (2018) Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics 19:684. https://doi.org/10.1186/s12864-018-5037-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim D, Paggi JM, Park C et al (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907–915. https://doi.org/10.1038/s41587-019-0201-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kobayashi A, Azuma K, Ikeda K, Inoue S (2020) Mechanisms underlying the regulation of mitochondrial respiratory chain complexes by nuclear steroid receptors. Int J Mol Sci 21. https://doi.org/10.3390/ijms21186683

Kobayashi A, Takeiwa T, Ikeda K, Inoue S (2023) Roles of noncoding RNAs in regulation of mitochondrial electron transport chain and oxidative phosphorylation. Int J Mol Sci 24(11):9414. https://doi.org/10.3390/ijms24119414

Kornienko AE, Dotter CP, Guenzl PM et al (2016) Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biol 17:14. https://doi.org/10.1186/s13059-016-0873-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kosinska-Selbi B, Mielczarek M, Szyda J (2020) Review: long non-coding RNA in livestock. Animal 14:2003–2013. https://doi.org/10.1017/S1751731120000841

Article  CAS  PubMed  Google Scholar 

Kovaka S, Zimin AV, Pertea GM et al (2019) Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol 20:278. https://doi.org/10.1186/s13059-019-1910-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lagarrigue S, Lorthiois M, Degalez F et al (2022) LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 33:248–270. https://doi.org/10.1007/s00335-021-09928-7

Article  CAS  PubMed  Google Scholar 

Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Q, Qiao J, Zhang Z et al (2020a) Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stress. Anim Biotechnol 31:9–16. https://doi.org/10.1080/10495398.2018.1521337

Article  CAS  PubMed  Google Scholar 

Li R, Li B, Jiang A et al (2020b) Exploring the lncRNAs related to skeletal muscle fiber types and meat quality traits in pigs. Genes (Basel) 11. https://doi.org/10.3390/genes11080883

Li T, Chen B, Yang P et al (2020c) Long non-coding RNA derived from lncRNA–mRNA co-expression networks modulates the locust phase change. Genom Proteom Bioinform 18:664–678. https://doi.org/10.1016/j.gpb.2020.05.001

Article  CAS  Google Scholar 

Mattay J (2023) Current technical approaches to study RNA–Protein interactions in mRNAs and long non-coding RNAs. BioChem 3:1–14. https://doi.org/10.3390/biochem3010001

Article  Google Scholar 

Mi H, Muruganujan A, Ebert D et al (2019) PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res 47:D419–D426. https://doi.org/10.1093/nar/gky1038

Article  CAS  PubMed  Google Scholar 

Miguel V, Lamas S, Espinosa-Diez C (2020) Role of non-coding-RNAs in response to environmental stressors and consequences on human health. Redox Biol 37:101580. https://doi.org/10.1016/j.redox.2020.101580

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morgulis A, Gertz EM, Schäffer AA, Agarwala R (2006) A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13:1028–1040. https://doi.org/10.1089/cmb.2006.13.1028

Article  CAS  PubMed  Google Scholar 

Muniz MMM, Simielli Fonseca LF, Scalez DCB et al (2022) Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle. Evol Appl 15:706–718. https://doi.org/10.1111/eva.13365

Article  CAS  PubMed  PubMed Central  Google Scholar 

Necsulea A, Soumillon M, Warnefors M et al (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505:635–640. https://doi.org/10.1038/nature12943

Article  CAS  PubMed  Google Scholar 

Pertea G, Pertea M (2020) GFF Utilities: GffRead and GffCompare. F1000Research 9. https://doi.org/10.12688/f1000research.23297.2

Petrov AI, Kay SJE, Kalvari I et al (2017) RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 45:D128–D134. https://doi.org/10.1093/nar/gkw1008

Article  CAS  PubMed  Google Scholar 

Qian Y, Shi L, Luo Z (2020) Long non-coding RNAs in cancer: implications for diagnosis, prognosis, and therapy. Front Med 7:612393. https://doi.org/10.3389/fmed.2020.612393

Article  Google Scholar 

Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. https://doi.org/10.1093/bioinformatics/btq033

Article  CAS  PubMed  PubMed Central  Google Scholar 

R Core Team (2013) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna. http://www.R-project.org/

Ren H, Li Y, Tang Z et al (2009) Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE libraries. Anim Genet 40:499–508. https://doi.org/10.1111/j.1365-2052.2009.01868.x

Article  CAS