Sequencing the large genomes of sharks. We focused on the brownbanded bamboo shark Chiloscyllium punctatum, for which we recently tabled embryonic stages 8 , and the cloudy catshark Scyliorhinus torazame. Their whole genomes, measured to be approximately 4.7 and 6.7 Gbp, respectively, were sequenced de novo to obtain assemblies including megabase-long scaffolds (Supplementary Note 1.1). We also assembled the genome of the whale shark Rhincodon typus using short sequence reads previously generated 3 (Supplementary Note 1.2). Using these genome assemblies, we performed genome-wide gene prediction, assisted by transcript evidence and protein-level homology to other vertebrates. The obtained genome assemblies and gene models exhibit high coverage (Supplementary Fig. 1), and of these, the bamboo shark genome assembly achieved the highest continuity (N50 scaffold length, 1.9 Mbp) and completeness (97% of reference orthologues identified at least partially). Using the novel gene models, we constructed orthologue groups encompassing a diverse array of vertebrate species (see below). Our products outperform existing

The heterogeneity and compartmentalization of stem cells is a common principle in many epithelia, and is known to function in epithelial maintenance, but its other physiological roles remain elusive. Here we show transcriptional and anatomical contributions of compartmentalized epidermal stem cells in tactile sensory unit formation in the mouse hair follicle. Epidermal stem cells in the follicle upper-bulge, where mechanosensory lanceolate complexes innervate, express a unique set of extracellular matrix (ECM) and neurogenesis-related genes. These epidermal stem cells deposit an ECM protein called EGFL6 into the collar matrix, a novel ECM that tightly ensheathes lanceolate complexes. EGFL6 is required for the proper patterning, touch responses, and αv integrin-enrichment of lanceolate complexes. By maintaining a quiescent original epidermal stem cell niche, the old bulge, epidermal stem cells provide anatomically stable follicle–lanceolate complex interfaces, irrespective of the stage of follicle regeneration cycle. Thus, compartmentalized epidermal stem cells provide a niche linking the hair follicle and the nervous system throughout the hair cycle.

31The heterogeneity and compartmentalization of stem cells is a common principle in many 32 epithelia, and is known to function in epithelial maintenance, but its other physiological 33 roles remain elusive. Here we show transcriptional and anatomical contributions of 34 compartmentalized epidermal stem cells (EpSCs) in tactile sensory unit formation in the 35 hair follicle (HF). EpSCs in the follicle upper-bulge, where mechanosensory lanceolate 36 complexes (LCs) innervate, express a unique set of extracellular matrix (ECM) and 37 neurogenesis-related genes. These EpSCs deposit an ECM protein EGFL6 into the collar 38 matrix, a novel ECM that tightly ensheathes LCs. EGFL6 is required for the proper 39 patterning, touch responses, and av integrin-enrichment of LCs. By maintaining a quiescent 40 original EpSC niche, the old bulge, EpSCs provide anatomically stable HF-LC interfaces, 41 irrespective of the stage of follicle regeneration cycle. Thus, compartmentalized EpSCs 42 provide a niche linking the HF and the nervous system throughout the hair cycle. 43 44 Results 95 Upper-bulge EpSCs are molecularly specialized for HF-nerve interactions 96We first examined the global transcriptional features of distinct EpSC populations in the 97 HF. To this end, we established FACS-based cell purification methods using several eGFP 98 reporter mouse lines that label different SC compartments to isolate cellular subpopulations 99 resident in the lower-isthmus (Lgr6 + ), upper-bulge (Gli1 + ), mid-bulge (CD34 + ), and hair 100 germ (Cdh3 + ) as well as unfractionated basal EpSCs (a6 integrin + ) ( Figure 1A and B, Figure 101

Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.