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Among chordate taxa, the cephalochordates diverged earlier than urochordates and vertebrates; thus, they retain unique, primitive developmental features. In particular, the amphioxus notochord has muscle-like properties, a feature not seen in urochordates or vertebrates. Amphioxus contains two  Brachyury  genes,  Bra1  and  Bra2 .  Bra2  is reportedly expressed in the blastopore, notochord, somites, and tail bud, in contrast to a low level of  Bra1  expression only in notochord. To distinguish the expression profiles of the two  Brachyury  genes at the single-cell level, we carried out single-cell RNA-seq (scRNA-seq) analysis using the amphioxus,  Branchiostoma japonicum . This scRNA-seq analysis classified  B. japonicum  embryonic cells into 15 clusters at developmental stages from midgastrula to early swimming larva.  Brachyury  was expressed in cells of clusters 4, 5, 8, and 9. We first confirmed that cluster 8 comprises cells that form somites since this cluster specifically expresses four myogenic factor genes. Cluster 9 contains a larger number of cells with high levels of  Bra2  expression and a smaller number of cells with  Bra1  expression. Simultaneous expression in cluster 9 of tool-kit genes, including  FoxA ,  Goosecoid , and  hedgehog , showed that this cluster comprises cells that form the notochord. Expression of  Bra2 , but not  Bra1 , in cells of clusters 4 and 5 at the gastrula stage together with expression of  Wnt1  and  Caudal  indicates that clusters 4 and 5 comprise cells of the blastopore, which contiguously form the tail bud. In addition,  Hox1, Hox3 , and  Hox4  were highly expressed in  Bra2 -expressing clusters 4, 5, 8, and 9 in a temporally coordinated manner, suggesting roles of anterior Hox genes in specification of mesodermal organs, including somites, notochord, and tail bud. This scRNA-seq analysis therefore highlights differences between the two  Brachyury  genes in relation to embryonic regions in which they are expressed and their levels of expression.  Bra2  is the ancestral  Brachyury  in amphioxus, since expression in the blastopore is shared with other deuterostomes. On the other hand,  Bra1  is a duplicate copy and likely evolved a supplementary function in notochord and somite formation in the  Branchiostoma  lineage.

A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum