In this study, we sequenced, annotated, and characterized the mitogenome of Tanichthys albiventris for the first time. The complete mitogenome is 16,544 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. We found nine genetic overlaps and 17 intergenic spacer regions throughout the mitogenome of T. albiventris . The A + T content of the mitogenome is 60.93%. All PCGs have the same start codon of the standard ATG, excepting for that of cytochrome c oxidase 1 ( cox1 ) which is the GTG. A phylogenetic analysis with another 15 species of the Cyprinidae was performed using MrBayes and IQtree, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that T. albiventris shares a close ancestry with Tanichthys albonubes .

A universal characteristic of eukaryotic transcription is that the promoter recruits RNAPII to produce both precursor mRNAs (pre-mRNAs) and short unstable promoter upstream transcripts (PROMPTs) toward the opposite direction. However, how the transcription machinery senses the correct direction to produce pre-mRNAs is largely unknown. Here, through multiple acute auxin-inducible degradation (AID) systems, we show that rapid depletion of a RNAPII-binding protein complex, Integrator, results in robust PROMPTsaccumulation throughout the genome. Interestingly, the accumulation of PROMPTs is compensated by the reduction of pre-mRNA transcripts in actively transcribed genes. Consistently, Integrator depletion alters the distribution of polymerase between the sense and antisense direction, which is marked by an increased RNAPII-CTD Tyr1 phosphorylation (Tyr1P) level at PROMPT regions and a refrained Ser2 phosphorylation (Ser2P) level at transcription start sites (TSSs). Mechanistically, the endonuclease activity of Integrator is critical to suppress PROMPTs production in a sequence-independent manner. During this step, the endonuclease activity can be inhibited by the U1 signal on nascent antisense transcripts through the recognition of the U1 snRNA-Integrator which relies on the U1-Integrator axis to govern the direction of gene transcription.

The complete mitogenome sequence of Coilia brachygnathus (Kreyenberg & Pappenheim, 1908) from Wabu Lake in Huai River Basin was annotated and characterized in this study. This mitochondrial genome is a circular DNA molecule of 16.896 bp in size with 57.52% AT content, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich region (control region) as other bony fishes. There are a total of 10 overlap locations and 15 intergenic spacer regions throughout the mitogenome of C. brachygnathus . All PCGs employed a standard ATG as a start codon, except cytochrome c oxidase 1 (cox1) with GTG. In addition, TAA or TAG was identified as the typical stop codon. A phylogenetic tree reconstructed with the maximum likelihood method depicted a clone relationship with eight species of genus Coilia and our previous study based on the amino acid sequences of 13 mitochondrial PCGs. The complete mitochondrial genome is a valuable resource in classifying and conserving C. brachygnathus .