S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.939, pp.403-410, 1990.

A. R. Amândio, A. Necsulea, J. E. Mascrez, B. Duboule, and D. , Hotair is dispensible for mouse 941 development, PLoS Genet, vol.12, p.1006232, 2016.

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, pp.943-106, 2010.

K. M. Anderson, D. M. Anderson, J. R. Mcanally, J. M. Shelton, R. Bassel-duby et al., Transcription 945 of the non-coding RNA upperhand controls Hand2 expression and heart development, Nature, vol.946, pp.433-436, 2016.

K. L. Ayers, N. M. Davidson, D. Demiyah, K. N. Roeszler, F. Grützner et al., 948 RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in 949 chicken and allows comprehensive annotation of the W-chromosome, Genome Biol, vol.14, 2013.

A. R. Barutcu, P. G. Maass, J. P. Lewandowski, C. L. Weiner, and J. L. Rinn, A TAD boundary is preserved upon 951 deletion of the CTCF-rich Firre locus, Nat Commun, vol.9, p.1444, 2018.

A. R. Bassett, A. Akhtar, D. P. Barlow, A. P. Bird, N. Brockdorff et al., , p.953

T. R. Gingeras and W. Haerty, Considerations when investigating lncRNA function in vivo, vol.954, p.3058, 2014.

S. Ben-tabou-de-leon and E. H. Davidson, Gene regulation: gene control network in development, 2007.

, Annu Rev Biophys Biomol Struct, vol.36, p.191

M. Blanchette, W. J. Kent, C. Riemer, L. Elnitski, A. Smit et al., Aligning multiple genomic sequences with the threaded blockset 959 aligner, Genome Res, vol.14, pp.708-715, 2004.

C. I. Brannan, E. C. Dees, R. S. Ingram, and S. M. Tilghman, The product of the H19 gene may function as an 961 RNA, Mol Cell Biol, vol.10, pp.28-36, 1990.

D. Brawand, M. Soumillon, A. Necsulea, P. Julien, G. Csárdi et al., , p.963

M. Kircher, The evolution of gene expression levels in mammalian organs, Nature, vol.964, pp.343-348, 2011.

N. L. Bray, H. Pimentel, P. Melsted, and L. Pachter, Near-optimal probabilistic RNA-seq quantification, 2016.

, Nat Biotechnol, vol.34, pp.525-527

C. J. Brown, A. Ballabio, J. L. Rupert, R. G. Lafreniere, M. Grompe et al., A gene from 968 the region of the human X inactivation centre is expressed exclusively from the inactive X 969 chromosome, Nature, vol.349, pp.38-44, 1991.

C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos et al., BLAST+: 971 architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009.

M. Cardoso-moreira, J. Halbert, D. Valloton, B. Velten, C. Chen et al., , p.973

S. Ovchinnikova, Gene expression across mammalian organ development, Nature, vol.974, pp.505-509, 2019.

F. N. Carelli, T. Hayakawa, Y. Go, H. Imai, M. Warnefors et al., The life history of retrocopies 976 illuminates the evolution of new mammalian genes, Genome Res, vol.26, pp.301-314, 2016.

J. Casper, A. S. Zweig, C. Villarreal, C. Tyner, M. L. Speir et al., The UCSC Genome Browser database, vol.46, pp.762-979, 2018.

M. Cesana, D. Cacchiarelli, I. Legnini, T. Santini, O. Sthandier et al., 981 A long noncoding RNA controls muscle differentiation by functioning as a competing 982 endogenous RNA, Cell, vol.147, pp.358-369, 2011.

D. Cortez, R. Marin, D. Toledo-flores, L. Froidevaux, A. Liechti et al., 984 Origins and functional evolution of Y chromosomes across mammals, Nature, vol.508, pp.488-93, 2014.

F. Cunningham, P. Achuthan, W. Akanni, J. Allen, M. R. Amode et al., Nucleic Acids Res, vol.47, pp.745-751, 2019.

W. F. Doolittle, We simply cannot go on being so vague about "function, Genome Biol, vol.19, p.223, 2018.

S. El-gebali, J. Mistry, A. Bateman, S. R. Eddy, A. Luciani et al., , p.989

A. Smart, The Pfam protein families database in 2019, Nucleic Acids Res, vol.47, pp.427-990, 2019.

J. M. Engreitz, J. E. Haines, E. M. Perez, G. Munson, J. Chen et al., Local regulation of gene expression by lncRNA promoters, transcription and splicing, Nature, vol.992, pp.452-455, 2016.

M. Goudarzi, K. Berg, L. M. Pieper, and A. F. Schier, Individual long non-coding RNAs have no overt 995 functions in zebrafish embryogenesis, viability and fertility, vol.8, 2019.

D. Graur, Y. Zheng, N. Price, R. Azevedo, R. A. Zufall et al., On the immortality of television sets: 997 "function" in the human genome according to the evolution-free gospel of ENCODE, Genome 998 Biol Evol, vol.5, pp.578-590, 2013.

C. D. Green, Q. Ma, G. L. Manske, A. N. Shami, X. Zheng et al., A comprehensive roadmap of murine spermatogenesis defined by single-cell RNA-1001, 2018.

. Seq, Dev Cell, vol.46, pp.651-667

A. F. Groff, D. B. Sanchez-gomez, M. Soruco, C. Gerhardinger, A. R. Barutcu et al., , p.1003

L. V. Sanchez and J. C. Lee, In vivo characterization of Linc-p21 reveals functional cis-1004 regulatory DNA elements, Cell Rep, vol.16, pp.2178-2186, 2016.

P. Grote and B. G. Herrmann, Long noncoding RNAs in organogenesis: making the difference, Trends 1006 Genet TIG, vol.31, pp.329-335, 2015.

P. Grote, L. Wittler, D. Hendrix, F. Koch, S. Währisch et al., The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall 1009 development in the mouse, Dev Cell, vol.24, pp.206-214, 2013.

M. Guttman, I. Amit, M. Garber, C. French, M. F. Lin et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs 1012 in mammals, Nature, vol.458, pp.223-227, 2009.

E. Hacisuleyman, L. A. Goff, C. Trapnell, A. Williams, J. Henao-mejia et al., , p.1014

M. Sauvageau and D. R. Kelley, Topological organization of multichromosomal regions by 1015 the long intergenic noncoding RNA Firre, Nat Struct Mol Biol, vol.21, pp.198-206, 2014.

W. Haerty and C. P. Ponting, Mutations within lncRNAs are effectively selected against in fruitfly but 1017 not in human, Genome Biol, vol.14, p.49, 2013.

W. Haerty and C. P. Ponting, No gene in the genome makes sense except in the light of evolution, Annu 1019 Rev Genomics Hum Genet, vol.15, pp.71-92, 2014.

W. Haerty and C. P. Ponting, Unexpected selection to retain high GC content and splicing enhancers 1021 within exons of multiexonic lncRNA loci, RNA N Y N, vol.21, pp.333-346, 2015.

V. Hamburger and H. L. Hamilton, A series of normal stages in the development of the chick embryo, J 1023 Morphol, vol.88, pp.49-92, 1951.

H. Hezroni, D. Koppstein, M. G. Schwartz, A. Avrutin, D. P. Bartel et al., Principles of long noncoding 1025 RNA evolution derived from direct comparison of transcriptomes in 17 species, Cell Rep, vol.11, pp.1026-1110, 2015.

M. K. Iyer, Y. S. Niknafs, R. Malik, U. Singhal, A. Sahu et al., The landscape of long noncoding RNAs in the human transcriptome, Nat Genet, vol.47, pp.1029-199, 2015.

H. Kaessmann, Origins, evolution, and phenotypic impact of new genes, Genome Res, vol.20, pp.1313-1031, 2010.

A. Kapusta, Z. Kronenberg, V. J. Lynch, X. Zhuo, L. Ramsay et al., , p.1033, 2013.

, Transposable elements are major contributors to the origin, diversification, and regulation of 1034 vertebrate long noncoding RNAs, PLoS Genet, vol.9, p.1003470

A. M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj et al., Many human large intergenic noncoding RNAs associate 1037 with chromatin-modifying complexes and affect gene expression, Proc Natl Acad Sci U S A, vol.106, pp.1038-11667, 2009.

D. Kim, B. Langmead, and S. L. Salzberg, HISAT: a fast spliced aligner with low memory requirements, Nat Methods, vol.12, pp.357-60, 1040.

C. Kutter, S. Watt, K. Stefflova, M. D. Wilson, A. Goncalves et al., Rapid 1042 turnover of long noncoding RNAs and the evolution of gene expression, PLoS Genet, vol.8, 2012.

P. A. Latos, F. M. Pauler, M. V. Koerner, H. B. ?energin, Q. J. Hudson et al., Airn transcriptional overlap, but not its lncRNA products, induces 1046 imprinted Igf2r silencing, Science, vol.338, pp.1469-1472, 2012.

Y. Liao, G. K. Smyth, and W. Shi, The R package Rsubread is easier, faster, cheaper and better for 1048 alignment and quantification of RNA sequencing reads, Nucleic Acids Res, 2019.

M. F. Lin, J. W. Carlson, M. A. Crosby, B. B. Matthews, C. Yu et al.,

S. E. Pierre, Revisiting the protein-coding gene catalog of Drosophila melanogaster 1051 using 12 fly genomes, Genome Res, vol.17, pp.1823-1836, 2007.

M. F. Lin, I. Jungreis, and M. Kellis, PhyloCSF: a comparative genomics method to distinguish protein 1053 coding and non-coding regions, Bioinforma Oxf Engl, vol.27, pp.275-282, 2011.

S. J. Liu, T. J. Nowakowski, A. A. Pollen, J. H. Lui, M. A. Horlbeck et al., , p.1055

A. A. Diaz, Single-cell analysis of long non-coding RNAs in the developing human 1056 neocortex, Genome Biol, vol.17, p.67, 2016.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq 1058 data with DESeq2, Genome Biol, vol.15, p.550, 2014.

A. C. Marques, J. Hughes, B. Graham, M. S. Kowalczyk, D. R. Higgs et al., Chromatin signatures at 1060 transcriptional start sites separate two equally populated yet distinct classes of intergenic long 1061 noncoding RNAs, Genome Biol, vol.14, p.131, 2013.

F. M. Mccarthy, K. Pendarvis, A. M. Cooksey, C. R. Gresham, M. Bomhoff et al., , p.1063

S. M. Bridges and S. C. Burgess, Chickspress: a resource for chicken gene expression, Database, 2019.

J. H. Mcdonald and M. Kreitman, Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.1067, pp.652-654, 1991.

M. Munschauer, C. T. Nguyen, K. Sirokman, C. R. Hartigan, L. Hogstrom et al., , p.1069

V. Subramanian and J. Chen, The NORAD lncRNA assembles a topoisomerase complex 1070 critical for genome stability, Nature, vol.561, pp.132-136, 2018.

A. Necsulea, M. Soumillon, M. Warnefors, A. Liechti, T. Daish et al., The 1072 evolution of lncRNA repertoires and expression patterns in tetrapods, Nature, vol.505, pp.635-640, 2014.

L. Nel-themaat, G. Gonzalez, H. Akiyama, and R. R. Behringer, Illuminating testis morphogenesis in the 1074 mouse, J Androl, vol.31, pp.5-10, 2010.

U. A. Ørom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini et al., , p.1076

Q. Huang, Long noncoding RNAs with enhancer-like function in human cells, Cell, vol.1077, pp.46-58, 2010.

M. Pertea, G. M. Pertea, C. M. Antonescu, T. Chang, J. T. Mendell et al., StringTie enables 1079 improved reconstruction of a transcriptome from RNA-seq reads, Nat Biotechnol, vol.33, pp.290-295, 2015.

M. Pertea, A. Shumate, G. Pertea, A. Varabyou, F. P. Breitwieser et al., , p.1081

S. L. Salzberg, CHESS: a new human gene catalog curated from thousands of large-scale 1082 RNA sequencing experiments reveals extensive transcriptional noise, Genome Biol, vol.19, p.208, 2018.

J. Ponjavic, C. P. Ponting, and G. Lunter, Functionality or transcriptional noise? Evidence for selection 1084 within long noncoding RNAs, Genome Res, vol.17, pp.556-65, 2007.

. R-core-team, R: A Language and Environment for Statistical Computing, 2018.

J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu et al., , p.1088

E. Segal, Functional demarcation of active and silent chromatin domains in human 1089 HOX loci by noncoding RNAs, Cell, vol.129, pp.1311-1323, 2007.

I. Sarropoulos, R. Marin, M. Cardoso-moreira, and H. Kaessmann, Developmental dynamics of lncRNAs 1091 across mammalian organs and species, Nature, vol.571, pp.510-514, 2019.

M. Sauvageau, L. A. Goff, S. Lodato, B. Bonev, A. F. Groff et al., Multiple knockout mouse models reveal lincRNAs are required 1094 for life and brain development, vol.2, p.1749, 2013.

A. Schüler, A. T. Ghanbarian, and L. D. Hurst, Purifying selection on splice-related motifs, not expression 1096 level nor RNA folding, explains nearly all constraint on human lincRNAs, Mol Biol Evol, vol.31, pp.3164-1097, 2014.

A. Siepel, G. Bejerano, J. S. Pedersen, A. S. Hinrichs, M. Hou et al., , p.1099

S. Richards, Evolutionarily conserved elements in vertebrate, insect, worm, and 1100 yeast genomes, Genome Res, vol.15, pp.1034-50, 2005.

D. Smedley, S. Haider, B. Ballester, R. Holland, D. London et al., BioMart--1102 biological queries made easy, BMC Genomics, vol.10, p.22, 2009.

A. Smit, R. Hubley, and P. Green, , 2003.

M. Soumillon, A. Necsulea, M. Weier, D. Brawand, X. Zhang et al., Cellular source and mechanisms of high transcriptome complexity in the 1106 mammalian testis, Cell Rep, vol.3, pp.2179-2190, 2013.

. Tabula-muris-consortium, Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris, Nature, vol.562, pp.367-372, 1108.

K. Theiler, The house mouse: atlas of embryonic development, 1110.

, UniProt: the universal protein knowledgebase, Nucleic Acids Res, vol.45, pp.1112-158, 2017.

S. Uebbing, A. Konzer, L. Xu, N. Backström, B. Brunström et al., Quantitative mass 1114 spectrometry reveals partial translational regulation for dosage compensation in chicken, Biol Evol, vol.32, pp.2716-2725, 1115.

I. Ulitsky, Evolution to the rescue: using comparative genomics to understand long non-coding 1117, 2016.

. Rnas, Nat Rev Genet, vol.17, pp.601-614

I. Ulitsky, A. Shkumatava, C. H. Jan, H. Sive, and D. P. Bartel, Conserved function of lincRNAs in vertebrate 1119 embryonic development despite rapid sequence evolution, Cell, vol.147, pp.1537-1550, 2011.

R. Vendramin, Y. Verheyden, H. Ishikawa, L. Goedert, N. E. Saraf et al., , p.1121

K. Izumikawa and P. Mestdagh, SAMMSON fosters cancer cell fitness by concertedly 1122 enhancing mitochondrial and cytosolic translation, Nat Struct Mol Biol, vol.25, pp.1035-1046, 2018.

D. Villar, C. Berthelot, S. Aldridge, T. F. Rayner, M. Lukk et al., , p.1124

A. J. Jasinska, Enhancer evolution across 20 mammalian species, Cell, vol.160, pp.554-566, 2015.

S. Washietl, M. Kellis, and M. Garber, Evolutionary dynamics and tissue specificity of human long 1126 noncoding RNAs in six mammals, Genome Res, vol.24, pp.616-644, 2014.

J. Zakany, F. Darbellay, B. Mascrez, A. Necsulea, and D. Duboule, Control of growth and gut maturation 1128 by HoxD genes and the associated lncRNA Haglr, Proc Natl Acad Sci U S A, vol.114, pp.9290-9299, 2017.