Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences

Accepted Manuscript Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences

Ramin Abdoli, Pouya Zamani, Maryam Ghasemi PII: DOI: Reference:

S2214-5400(17)30084-1 doi:10.1016/j.mgene.2017.10.004 MGENE 370

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ACCEPTED MANUSCRIPT Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences Ramin Abdoli, Pouya Zamani*, Maryam Ghasemi Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran

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* Corresponding author. E-mail address: [email protected]

ABSTRACT

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Mitochondrial genome (mitogenome) is a small and extra-chromosomal DNA, located in cytoplasm and presents an ideal model to study evolution and genetic similarity due to

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genomic rearrangement. In the present study, mitochondrial DNA sequences of 14 farm animal species including, Bos indicus, Bos taurus, Ovis aries, Capra hircus, Equus caballus,

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Camelus bactrianus, Camelus dromedaries, Sus scrofa domesticus, Gallus gallus, Meleagris gallopavo, Struthio camelus, Anser anser, Anas platyrhynchos and Oncorhynchus mykiss

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were retrieved from NCBI databases and compared with the sequence of Homo sapiens. Sequence distance analysis showed a high similarity (74.4%) between Homo sapiens and Equus caballus, while the Oncorhynchus mykiss had the lowest similarity (64.1%) to the

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Homo sapiens. The highest similarities among the studied species were observed between

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Anser anser and Anas platyrhynchos (100%) and Bos taurus and Bos indicus (98.5%). In phylogenetic analysis, the Homo sapiens fell in a same cluster with Equus caballus, Bos indicus, Bos taurus, Ovis aries, Capra hircus, Camelus bactrianus, Camelus dromedaries and

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Sus scrofa domesticus. Poultry species (Gallus gallus, Meleagris gallopavo and Struthio camelus, Anser anser and Anas platyrhynchos) and rainbow trout (Oncorhynchus mykiss)

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formed a distinct cluster with the lowest similarity to the human. The D-loop regions showed the most obvious differences, while other parts including tRNA, rRNA, STSs and CDSs for different genes, had more similarities. Based on the results of the present study, the mitogenomic sequences could be used for accurate phylogenetic analysis and clustering of different species. Moreover, use of mitogenomic sequence in mammalian farm animals, as biomedical model species would not be far-fetched for genetic control of zoonotic diseases.

Keywords: Mitochondrial genome; Human; Livestock; Phylogenetic analysis

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ACCEPTED MANUSCRIPT 1. Introduction Generally, phylogenetic approaches help to answer some questions such as relationships among species or genes, origin of viral infection and patterns of demographic changes and migration of species (Yang and Rannala, 2012). Classical phylogenetic approach is based on morphological characteristics of organisms, while molecular approaches use DNA and RNA

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nucleotides or protein amino acid sequences for construction of phylogeny trees (Patwardhan

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et al., 2014). In modern phylogenetic approaches, the phylogenetic distances are estimated

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based on the observed differences in the studied sequences (either DNA, RNA or proteins). Genomic materials used in phylogenetic studies could be obtained from chromosomal DNA

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in nucleus and extra chromosomal DNA, which could be found in eukaryotes organelles such as mitochondria and chloroplasts.

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Mitochondrion is an organelle located in cytoplasm, outside the nucleus, containing some genetic information. The mitochondrial genome (mitogenome) is constituted by

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mitochondrial DNA (mtDNA), which contains a limited number of genes. The mtDNA is

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transmitted to offspring by dam and is commonly used in molecular phylogenetic studies (Moritz et al., 1978). Complete mitogenome of Homo sapiens is about 16569 bp in length

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(Andrews et al., 1999). The mtDNA is also a small genome in animals (15 - 20 kb, typically about 16 kb as an average) containing 37 genes with a few exceptions (Boore, 1999).

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Generally, mitogenome studies started many years ago. By accumulation of whole genome sequencing projects and increasing evidences on mitochondrial genes transfer into the nucleus, occurrence and phylogenetic studies on nuclear mitochondrial-like sequences (NUMTS) constitutes an important aspect of many studies (Bernt et al., 2013). Mitochondrial sequences have been used for phylogenetic reconstructions of breed origin in domestic animals during the last decade in several studies (Cieslak et al., 2010; Groeneveld et al., 2010; Lenstra et al., 2012; Ludwig et al. 2013) and use of mtDNA is increasingly 2

ACCEPTED MANUSCRIPT becoming popular in population genetic and phylogenetic studies (Patwardhan et al., 2014). On the other hand, there are several important zoonotic diseases, which their severity and transmission could be affected by genetic similarity of human and host animal, because disease resistance could be noticeably affected by genetic factors (Bishop et al., 2011). The mitogenome is extremely smaller than the nuclear genome but presents unique clinical

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and experimental challenges, whereas the mtDNA mutations are important causes of

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inherited diseases (Taylor and Turnbull, 2005) and cause a variety of pathologic states in

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human patients (Dunn et al., 2012). Thus, degree of mtDNA similarity could be an important factor affecting genetic susceptibility to the diseases transmitting between human and farm

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animal species. The aim of this study was to identify genetic similarity and phylogenetic analysis of human and several farm animals based on mitochondrial DNA sequences.

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2. Methods 2.1. Data description

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Nucleotide sequences of mtDNA for 14 farm animal species, including humped cattle, Bos

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indicus (NCBI RefSeq Nucleic NC_005971, 16341 bp); taurine cattle, Bos taurus (NCBI RefSeq Nucleic NC_006853, 16338 bp); sheep, Ovis aries (NCBI RefSeq Nucleic

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NC_001941, 16616 bp); goat, Capra hircus (NCBI RefSeq Nucleic NC_005044, 16643 bp); horse, Equus caballus (NCBI RefSeq Nucleic NC_001640, 16660 bp); Bactrian camel,

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Camelus bactrianus (NCBI RefSeq Nucleic NC_009628, 16659 bp); dromedary camel, Camelus dromedarius (NCBI Reference Sequence: NC_009849, 16643 bp); domestic pig, Sus scrofa domesticus (NCBI RefSeq Nucleic NC_012095, 16670 bp); chicken, Gallus gallus (NCBI RefSeq Nucleic NC_001323, 16775 bp); turkey, Meleagris gallopavo (NCBI RefSeq Nucleic NC_010195, 16719 bp); ostrich, Struthio camelus (NCBI RefSeq Nucleic NC_002785, 16595 bp); goose, Anser anser (NCBI Reference Sequence: NC_011196, 16738 bp); duck, Anas platyrhynchos (NCBI Reference Sequence: NC_009684, 16604 bp) and 3

ACCEPTED MANUSCRIPT rainbow trout, Oncorhynchus mykiss (NCBI RefSeq Nucleic NC_001717, 16642 bp) were retrieved from NCBI databases (https://www.ncbi.nlm.nih.gov) and compared with sequence of human, Homo sapiens (NCBI RefSeq Nucleic NC_012920, 16569 bp). 2.2. Genetic similarity and phylogenetic analysis Nucleotide sequence alignments were carried out using MegAlign module of DNASTAR

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software (DNASTAR Lasergene Inc., Madison, WI. USA) and compared by CLUSTAL W

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method. When sequences were added to a MegAlign project, they were arranged in a window

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called Worktable which data manipulation is performed. The Worktable displays sequence names alongside two panes which initially display left and right ends of the alignment.

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MegAlign generates pairwise and multiple sequence alignments of DNA or protein or a combination of the both, quickly and accurately. Four algorithms are available for pairwise

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alignments: Martinez, Needleman-Wunsch and Wilbur-Lipman for DNA alignments and Lipman-Pearson for protein alignments. Four additional algorithms including Jotun Hein,

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Clustal V and two Clustal W options (Slow-Accurate and Fast-Approximate) are also

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available for multiple alignments. The Clustal W method was used for multiple comparisons, as an accurate, popular and practical approach in the category of hierarchical methods

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(Thompson et al., 1994). The Sequence Distances section in the DNASTAR was used for calculation nucleotide sequences of similarities. In this software, the residue substitutions

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window displays a table to show the number of residue substitutions predicted to have occurred to give rise to the sequence differences in the current alignment (DNASTAR Lasergene Inc., Madison, WI. USA). The phylogenetic tree was constituted for the studied species, based on maximum likelihood method and using MEGA 7 software (Kumar et al., 2016). In this software, the predicted phylogenetic relationship between the aligned sequences, is displayed in a phylogenetic tree

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ACCEPTED MANUSCRIPT window. The bootstrap consensus tree inferred from 1000 replicates was used to represent the evolutionary history for the studied species.

3. Results and discussion The results of the nucleotide alignment analysis as sequence similarities between the mtDNA of Homo sapiens and those reported for other studies species (Bos indicus, Bos taurus, Ovis

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aries, Capra hircus, Equus caballus, Camelus bactrianus, Camelus dromedaries, Sus scrofa

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domesticus, Gallus gallus, Meleagris gallopavo, Struthio camelus, Anser anser, Anas

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platyrhynchos and Oncorhynchus mykiss) are presented in Table 1. Nucleotide sequence similarities, higher than 72% were found between the sequence of Homo sapiens and those of

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eight mammalian species (Bos indicus, Bos taurus, Ovis aries, Capra hircus, Equus caballus, Camelus bactrianus, Camelus dromedaries and Sus scrofa domesticus). The Equus caballus

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had the highest similarity (74.4%) and the Oncorhynchus mykiss had the lowest similarity (64.1%) to the Homo sapiens. The highest similarities among the studied species were

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observed between Anser anser and Anas platyrhynchos (100%) and Bos taurus and Bos

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indicus (98.5%). High similarities (77.3 – 100%) were observed between poultry species (Gallus gallus, Meleagris gallopavo, Struthio camelus, Anser anser and Anas platyrhynchos).

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Based on the alignment analysis, the most obvious differences between species in terms of mitogenomic sequences were attributed to the D-loop regions, which included the beginning

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and the end of each sequence. Other parts of the mtDNA, including tRNA, rRNA, STSs and CDSs for different genes, had more similarities in comparison to the D-loop sequences. High similarity of poultry species was also observed in phylogenetic tree analysis which poultry species constituted a distinct cluster (Figure 1). The phylogenetic tree identified two main clusters in which the mammalian species (human, humped cattle, taurine cattle, sheep, goat, horse, Bactrian camel, dromedary camel and domestic pig) were distinctly separated from poultry species (chicken, turkey, ostrich, goose 5

ACCEPTED MANUSCRIPT and duck) and rainbow trout (Figure 1). Moreover, cattle species (Bos indicus and Bos taurus), sheep and goat (Ovis aries and Capra hircus), camel species (Camelus bactrianus and Camelus dromedaries) poultry species (Gallus gallus, Meleagris gallopavo, Struthio camelus, Anser anser and Anas platyrhynchos) and rainbow trout (Oncorhynchus mykiss) were clustered in separate groups (Figure 1). Thus, it seems that the phylogenetic analysis

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based on mitogenomic sequences results in an accurate clustering of the studied species.

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In animals, mitochondrial genome contains 37 genes, including two ribosomal RNA genes,

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22 RNA transport genes, and 13 genes encoding respiratory chain proteins (Boore, 1999). The only non-coding fragment in the mtDNA is the D-loop sequence (approximately 1100 bp

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in length) which accounts for less than 7% of the mitochondrial genome with the highest degree of polymorphism in mitogenome and comprising a promoter for strand H and L

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transcription and a signal triggering replication of the H-strand (Ślaska et al., 2014). It has been demonstrated that the mtDNA polymorphisms have some correlations with production

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and reproduction traits in farm animals (Mannen et al., 2003; Yen et al., 2007; Reicher et al.,

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2012). On the other hand, mutation rate in the mtDNA is much higher than chromosomal DNA and the mtDNA is often used in phylogenetic studies and determination of genetic

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distances between different taxa (Ludwig et al., 2013; Ślaska et al., 2014). Mitochondrial sequences have been used to study breed origins of different farm animals

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such as horses (Cieslak et al., 2010; Georgescu et al., 2011), chicken (Lee et al., 2007; Dancause et al., 2011; Gao et al., 2017), cattle (Cai et al., 2007; Kim et al., 2013; Lenstra et al., 2014), sheep (Tapio et al., 2006; Pariset et al., 2011; Demirci et al., 2013) and goat (Piras et al., 2012; Doro et al., 2014; Colli et al., 2015). Analysis of mtDNA in modern sheep breeds showed separate ancestral origins for European and Asian domestic sheep (Hiendleder et al., 1998). A phylogenetic study based on mitochondrial DNA sequences showed multiple centers of pig domestication across Eurasia

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ACCEPTED MANUSCRIPT (Larson et al., 2005) and another study, using mtDNA sequences showed independent domestication of pigs in Asia and Europe (Fang and Anderson, 2006). In this study, the clustering results of the phylogenetic tree were surprisingly accordant to studies based on nuclear DNA and the conceptual distinction of the studied species. In a study comparing the human and cattle (Bos Taurus) genomes, 14 cattle chromosomes were

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painted in their entirety by the same human chromosomes, and human 13, 17 and X

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chromosomes, not entirely but also exclusively painted bovine 12, 19 and X chromosomes,

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respectively (Solinas-Toldo et al., 1995). In a study, cattle and human genomes were compared and among a total of 768 genes on the cattle radiation hybrid map, 687 genes

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(89.5%) had putative human orthologs and the remaining 81 genes (10.5%) were expressed sequence tags or database sequences that had no significant human hits in UniGene (Band et

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al., 2000). In another study, comparing pig (Sus scrofa domesticus( and human genomes, four porcine chromosomes had homologous segments originating from at least four to five human

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chromosomes, two porcine chromosomes each had homologous segments corresponding to

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three different human chromosomes and the remaining chromosomes showed segmental homology to one or two human chromosomes (Frönicke et al., 1996). In another survey

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comparing human and sheep (Ovis aries) nuclear genomes by fluorescence in situ hybridization (FISH), the painting results on sequentially stained RBA-banded preparations

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showed a high proportion of conserved regions between human and sheep genomes, whereas 48 human chromosome segments were detected in ovis aries chromosomes (Iannuzzi et al., 1999). Phylogenetic distribution of mitochondrial haplotypes, which are sets of polymorphisms derived from a common ancestor, indicated an African origin of human mtDNA with seven major groups, L0 to L6 (Ślaska et al., 2014). In another study, some parts of mitochondrial coding sequences, but not all, were used for phylogenetic analysis of 60 mammalian species

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ACCEPTED MANUSCRIPT and the results challenged several traditional or semi-traditional morphological hypotheses about eutherian relationships and almost different rooting points in eutherian tree, compared to other mitochondrial/nuclear studies (Arnason et al., 2002).

4. Conclusion According to the results of the present study it could be concluded that the mitochondrial

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genomic sequences could be used for accurate phylogenetic analysis and clustering of

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different species. In this study high mitogenomic similarities were found between human and

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several farm animal taxa including horse, camel, pig, sheep, goat and cattle, with the highest similarity to the horses. However, poultry species (chicken, turkey, ostrich, goose and duck)

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and rainbow trout formed distinct clusters with the lowest similarity to the human. Thus, it seems that more emphasis should be placed on mitochondrial genomic factors for genetic

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control of zoonotic diseases between human and mammalian farm animals.

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Table 1 Similarity and divergence percentages of the mtDNA of Homo sapiens and reported nucleotide sequences for farm animals.

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Figure 1 Molecular phylogenetic tree of the mtDNA of Homo sapiens and reported nucleotide sequences for the studied species by maximum likelihood method. Numbers at the nodes represent the percent bootstrap values for interior branches after 1000 replications.

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