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The complete mitogenome of a lorikeet, Trichoglossus rubritorquis (Psittaciformes, Loriidae), was determined first in the genus Trichoglossus . The assembled mitogenome was 17,915 bp and composed of 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. Nucleotide composition of T. rubritorquis mitogenome was 30.20% A, 33.30% C, 14.04% G, and 22.46% T, with an A + T bias of 52.66%. ML tree based on 13 protein-coding genes indicated that, Melopsittacus undulatus of the family Psittacidae was the closest related species to T. rubritorquis . This result suggested that lorikeets might still be in the family Psittacidae., Competing Interests: No potential conflict of interest was reported by the authors., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The first complete mitogenome of Hong Kong paradise fish ( Macropodus hongkongensis ) was determined in this study. The assembled mitogenome is 16,494 bp and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition of the complete mitogenome is 30.6% A, 24.8% C, 14.8% G, and 29.8% T, with an A + T bias of 60.4%. The maximum-likelihood tree based on 13 protein-coding genes showed that M. erythropterus was the closest related species to M. hongkongensis ., Competing Interests: The authors declare that there is no conflict of interest., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The complete mitochondrial genome of Lumbricus rubellus was analyzed by next-generation sequencing. The mitogenome was 15,464 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and a non-coding region. The phylogenetic analysis of 13 PCGs within the class Oligochaeta suggested that L. rubellus was placed as sister to L. terrestris of the same genus. The results obtained here can contribute to the phylogenetic analysis of earthworms., Competing Interests: No potential conflict of interest was reported by the authors., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The relationship between CpG content and DNA methylation has attracted considerable interest in recent years. Direct or indirect methods have been developed to investigate their regulatory functions based on various hypotheses, large cohort studies, and meta-analyses. However, all of these analyses were performed at units of CpG blocks and, thus, the influence of finer genome structure has been neglected. Herein, we present a novel algorithm of base-pair resolution to systematically investigate the relationship between CpG contents and DNA methylation. By introducing the concept of 'complementary index' we examined the methylomes of 34 adult and 7 embryonic tissues and successfully fitted the relationship of DNA methylation and CpG density into a nonlinear mathematical model. A further algorithm was developed to locate the regions where CpG density does not match expectations from the model, termed 'conflict of gap' (COG) regions. Interestingly, COGs are highly concordant in human and mouse and their distributions display a tissue-specific pattern. Based on COG methylation patterns we correctly classified tissues according to their function or origin. We demonstrate that COGs based on our method can reveal more and deeper information than traditional differential methylation region (DMR) approaches. We also found that when COGs are located near to transcription start site (TSS), these regions can determine which promoters will be utilized for initiating gene transcription. Furthermore, COGs located far from the TSS perform as enhancers in terms of histone modification, sequence conservation, transcription factor binding, and DNase I-hypersensitivity.