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In the field of computational biology, genome sequence comparison among different species is essential and has applications in both the research and scientific fields. Owing to the lengthy processing time and large number of data sets, the alignment-based approaches are unsuitable and ineffective. Therefore, alignment-free techniques have obtained popularity for acquiring proper sequence clustering and evolutionary relationship among species. In this paper, a complete bipartite graph based Positional difference and Frequency (PdF) vector descriptor is introduced. Positional difference and Frequency, two parameters, are applied to the genome sequence to create a 16- dimensional vector descriptor using the di-nucleotide representation of genome sequence. Subsequently, a distance matrix is calculated to construct the phylogenetic trees for different data sets of mammals and viruses. The achieved outcomes are compared with the phylogenetic trees of the earlier methods viz. the FFP method, the ClustalW method, the MEV method, the PCNV method and the FIS method. In most instances, the proposed method produces more precise outcomes than the preceding techniques and has potential for genome sequence comparison on both the equal and unequal length of data-sets.Communicated by Ramaswamy H. Sarma.

In this study, we sequenced the complete mitogenome of Kentrochrysalis streckeri (Staudinger, 1880). The complete mitogenome sequence of K. streckeri is circular, 15,253 bp in size and contains 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). Nucleotide composition was A + T biased, and all the PCGs exhibited a positive AT-skew, which was reflected in the nucleotide composition, codon, and amino acid usage. Most PCGs start with ATG or ATT and stop with TAA. However, COX1 gene starts with CGA and three genes ( COX1 , COX2 , NAD5 ) use the incomplete stop codon T. Phylogenetic analyses showed that the relationship ( K. streckeri +(( Manduca sexta + Sphinx morio )+( Psilogramma increta +( Psilogramma menephron + Notonagemia analis scribae ))))., Competing Interests: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper., (© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

We report the complete mitochondrial genome of the firefly Curtos fulvocapitalis Jeng et Yang 1998. The circular genome is 16,398 bp and has a base composition of A (42.21%), C (11.22%), G (7.73%), and T (38.85%). Our sequence is similar to those of other metazoans, which contain 13 protein-coding genes. All 13 protein-coding genes were initiated by the ATN (ATT, ATA, and ATG) codon. Nine protein-coding genes stopped with TAA or TAG codons, and the other four genes had an incomplete termination codon, a single T. We sequenced the mitochondrial genome of fireflies to analyze phylogenetic relationships and determine the evolution of their flashing signals., Competing Interests: The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

In order to fully comprehend the evolution and kinship of fishes in the family of Loricariidae, the complete mitochondrial genome of the Loricariidae fish Ancistrus temmincki was firstly characterized in the present study. The whole mitogenome was 16,657 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs genes, a control region and origin of light-strand replication. The proportion of coding sequences with a total length of 11,473 bp was 68.88%, which encoded 3,813 amino acids. The genome composition was highly A + T biased (56.29%), and exhibited AT-skew (0.0661) and a negative GC-skew (-0.2740). All protein-coding genes were started with ATG except for GTG in CO1, while stopped with the standard TAN codons or a single T. The control region (D-loop) ranging from 15,635 bp to 16,657 bp was 1023 bp in size. Until now, there is hardly any studies on the complete mitochondrial sequence in the genus of Ancistrus , phylogenetic analysis showed that A. temmincki was most closely related to Ancistrus cryptophthalmus in the genus of Ancistrus . The complete mitochondrial genome sequence has provided a new insight into the taxonomic classification, and a more complex picture of the species diversity within the family of Loricariidae., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The complete chloroplast genome sequence of Chaenomeles cathayensis and Chaenomeles thibetica was characterized from Illumina pair-end sequencing. The length of C . cathayensis and C . thibetica chloroplast genome of was 159,875 bp and 159,907 bp, respectively. The C . cathayensis chloroplast genome contained a large single-copy region (LSC) of 87,813bp, a small single-copy region (SSC) of 19,304 bp, and two inverted repeat (IR) regions of 26,379 bp, which is a quadripartite structure. Similarity, The C . thibetica chloroplast genome also contained a quadripartite structure, including a LSC region (87,851 bp), a SSC region (19,298 bp), and two IR regions (26,379 bp). The overall GC content of C . cathayensis and C . thibetica are both 36.57%. The C . cathayensis and C . thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The C . thibetica chloroplast genome contains 130 complete genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The neighbour-joining phylogenetic analysis showed that C . cathayensis and C . thibetica clustered together, indicated that C . cathayensis and C . thibetica have closed evolutionary relationship compared with other Chaenomele s species., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Xanthium sibiricum is a common and annual the Traditional Chinese Medicine for many years in China. In this study, we presented the complete chloroplast genome of X. sibiricum . The chloroplast genome size was 151,897 bp in length that contained a large single-copy region (LSC) of 83,847 bp, a small single-copy region (SSC) of 17,890 bp and two inverted repeat regions (IR) of 25,080 bp. The overall nucleotide composition of the chloroplast genome is: 31.2% of A, 31.3% T, 18.5% C and 19.0% G, with a total G + C content of the chloroplast genome 37.5% and A + T of 62.5%. The chloroplast genome of X. sibiricum contains 133 genes, which included 88 protein-coding genes (PCG), 37 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic neighbour-joining (NJ) analysis result shown that the position of X. sibiricum closely related to X. strumarium in evolutionary relationship., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The muskrat Ondatra zibethicus is native to North America, However it has successfully dispersed into most areas of northeast China in the past decades, which may lead to potential impact on endemic eco-system. We determined and annotated the whole mtDNA genome of the muskrat O. zibethicus to better understand the evolutionary relationship of this invasive species with other Rodentia distributed in China. The complete mitogenome is 16,351 bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. We built the phylogenetic tree of muskrat and other 11 most closely related Rodentia species., Competing Interests: No potential conflict of interest was reported by the authors., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The fruit of Cinnamomum cassia is an important spice material and its branch is a common Chinese herbal medicine as the family Lauraceae. In this study, we reported the complete chloroplast genome of C. cassia. The chloroplast genome of C. cassia with length of 152,675 bp is a characteristic quadripartite structure. The length of the inverted-repeats regions (IRs), large single-copy (LSC) region, and small single-copy (SSC) region of C. cassia was 20,068 bp, 93,663 and 18,876 bp. The chloroplast genome of C. cassia contains 124 genes, which includes 80 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs) and 8 ribosomal RNA genes (rRNAs). The overall nucleotide content of the chloroplast genome: 30.0% A (Adenine), 30.8% T (Thymine), 19.7% C (Cytosine), 19.5% G (Guanine), and 39.2% GC content. Evolutionary relationship result showed that Cinnamomum cassia was most closely related to Cinnamomum parthenoxylon in the family Lauraceae by the Neighbor-Joining (NJ) method., Competing Interests: The authors have declared that no competing interests exist., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

In the present study, we reported the complete mitochondrial genome of medical pipefish Doryichthys boaja Bleeker 1850. The complete mitochondrial genome of D. boaja was 16,562 bp in length and had a base composition of A (31.10%), C (24.14%), G (14.36%), and T (30.40%). Similar to other Syngnathidae species, it contained a typically conserved structure, including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The 13 protein-coding genes encoded 3800 amino acids in total, most of which used the initiation codon ATG except CO1 gene started with GTG. For the stop codon, 6 genes applied TAA as the stop codon, while the other 7 genes used an incomplete stop codon T or TA. The lengths of 12S rRNA and 16S rRNA were 941 bp and 1671 bp, respectively. The control region of D. boaja ranged from 15,615 bp to 16,562 bp, which was 948 bp in length. The complete mitochondrial genome of D. boaja provided essential and important molecular data for phylogeography and evolutionary analysis of Syngnathidae Family., Competing Interests: No potential conflict of interest was reported by the authors.., (© 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

In the present study, we report the complete mitochondrial genome of Jayakar's seahorse, Hippocampus jayakari Boulenger, 1900. The genome of H. jayakari is found to be 16,520 bp in length and has a base composition of A (32.82%), C (23.28%), G (14.13%), and T (29.67%). Similar to other Hippocampus species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The protein-coding genes had ATG or GTG as the initiation codon and only 6 genes (COX1, ATP8, ATP6, ND4L, ND5 and ND6) terminated by the complete typical stop codon TAA. The lengths of 12S rRNA and 16S rRNA are 939 bp and 1686 bp, respectively. All tRNA genes typically formed a cloverleaf secondary structure, except for tRNA-Ser containing a dihydrouridine arm replacement loop. Hippocampus jayakari exhibited a relatively distant genetic relationship with other 13 Hippocamupus species according to the phylogenetic analysis. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of Hippocamupus and conservation genetics of H. jayakari ., Competing Interests: The authors declare no conflict of interest in the preparation and execution of this manuscript., (© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The American mink, Neovison vison , is native to North America and listed as one of the most widely distributed invasive species into the Eurasian mainland. Even though facing serious over-hunting and habitat degradation problems, this species has successfully dispersed into most areas of northeast China in the past decades, which may have a huge impact on local species composition and structure. We determined and annotated the whole mitochondrial DNA genome of the American mink N. vison to better understand the evolutionary relationship of this invasive species with other Mustelidae distributing in China. The complete mitogenome is 16 627 bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. We built the phylogenetic tree of American mink and other 10 most closely Mustelidae species., Competing Interests: The authors declare no conflict of interests. The authors alone are responsible for the content and writing of the paper. This study was supported by Heilongjiang Province Science Foundation for Youths (QC2011C091)., (© 2016 The Author(s). Published by Taylor & Francis.)