The Complete Mitochondrial Genome from Iraqi Meriz Goats and the Maternal Lineage Using Whole Genome Sequencing Data

Iranian Journal of Applied Animal Science

دوره 12، شماره 2، شهریور 2022، صفحه 321-328   

نوع مقاله: Research Articles

نویسندگان

S.I. Ihsan Mustafa^{* 1}؛ J.S. Heslop-Harrison²؛ T. Schwarzacher²

¹Department of Animal Production, College of Agricultural Engineering Science, University of Duhok, Kurdistan Region, Iraq

²Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom

چکیده

Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive traits of the Meriz goat have been described, the complete mitochondrial genome, maternal lineage, and genetic diversity of the breed have yet to be identified. Therefore, the whole genome sequencing data and bioinformatics analysis were used to assemble the complete mitochondrial genome, generate a maternal phylogeny, and identify some mitogenomic diversity features of Meriz goats Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive traits of the Meriz goat have been described, the complete mitochondrial genome, maternal lineage, and genetic diversity of the breed have yet to be identified. Therefore, the whole genome sequencing data and bioinformatics analysis were used to assemble the complete mitochondrial genome, generate a maternal phylogeny, and identify some mitogenomic diversity features of Meriz goats from the Iraqi Kurdistan region. The complete mitochondrial genome of the two individuals was assembled with lengths of 16641 and 16639 bp, respectively (MH165338 and MH165339). The mitogenome comprises13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and one non-coding control region. In addition, our data revealed that the mitogenome copy number is greater in female goats than in males. Integration into a phylogenetic tree with other goat breeds showed that Meriz goats belong to the most predominant maternal haplogroup A (_HPGA). Furthermore, nucleotide diversity and mitogenomic analysis indicated that Meriz goats have a high level of mitogenomic similarity to Chinese Cashmere goats and Turkish Angora goats within the same maternal lineage. The molecular data reported here provide useful insights into the evolutionary relationships and mitogenomic diversity of domestic and wild goats from the center of diversity of animal species in the Middle East.

کلیدواژه‌ها

capra؛ genetic diversity؛ mitogenome copy number؛ next generation sequencing؛ phylogeny

اصل مقاله

INTRODUCTION

The domestic goat (Capra hircus) is in the Caprini tribe, Caprinae subfamily, of the Bovidae family in the order Artiodactyla. The domestic goat was among the first group of the oldest domesticated species of livestock (Zeder, 2008). Zooarchaelogical data and evidence indicated that the farming process (domestication) of goat was started around 10000-11000 years before the present (YBP) in the Fertile Crescent area, in particular in the long range of Zagros mountains, covering parts of Western Asia, Iran, North-East Iraq and southeastern Turkey (Naderi et al. 2008; Zeder, 2008; Colli et al. 2015). According to the molecular genetics data, Daly et al. (2018) demonstrated that the current genetically and geographically distinct goat populations were domesticated from multiple divergent wild goat sources. At present, the population of domestic goats exceeds 1 billion which are distributed across geographically different regions worldwide (reviewed in Amills et al. 2017). In Iraq, the native goats are mainly raised for milk and meat production, while their hair is of secondary significance. In 1999, the populations of the native goats were about 1.3 million head (FAO, 2000). Recent data indicated that about 43.3%, 44.2% and 12.5% of native goats are distributed in the northern, central and southern parts of Iraq (Alkass and Jurna, 2005). Meriz (Maraz or Cheer) is one of the indigenous goat breeds found in the mountainous altitude regions (with poor grazing habitats) of the Kurdistan region of Iraq in the Fertile Crescent area, and is raised for meat, milk and fiber production. The economically important breed produces valuable fine outercoat fibers which are mainly used for manufacture of Kurdish traditional costume (Alkass and Juma, 2005). Cashmere producing goats are found in several countries such as China, Iran, Afghanistan, Mongolia and India in which China has highest production of Cashmere than any other country (Shakyawar et al. 2013; Seki et al. 2011; Wang et al. 2013). The evolutionary biology of mitochondrial DNA (mtDNA) fragments have been widely investigated and used as markers for documentation of many species (Tillmar et al. 2013; Yang et al. 2014; Lv et al. 2015; Harley et al. 2016; Mannen et al. 2020). Phylogenetic relationships based on the diversity of maternal lineages can be used to revolve ancestry and origins of different domesticated animals by studying nucleotide polymorphisms within mitochondrial DNA sequences (Meadows et al. 2007; Achilli et al. 2009; Lippold et al. 2011; Osman et al. 2021). In goats, phylogenetic analyses based on either control region sequences or complete mitochondrial genome (mitogenome) classified multiple maternal lineages and represented in the six major monophyletic mtDNA haplogroups (_HPG); _HPGA, _HPGB, _HPGC, _HPGD, _HPGF, and _HPGG; of which _HPGA was predominant and widespread in goats worldwide (Naderi et al. 2007; Colli et al. 2015). Despite the central location of Iraq in the Fertile Crescent, it is notable that there has not been any recordregarding mitogenomic diversity and phylogenetic position inMeriz goats. Therefore, in this study, we aimed to assemblethe complete mitochondrial genome (mitogenome), identifymaternal phylogeny and estimate mitogenomic diversity of theIraqi Meriz goats using Next Generation Sequencing (NGS)data.

 

MATERIALS AND METHODS

Sampling and isolation of genomic dna

The whole blood was sampled with K2E Vacutainers (Becton Dickinson, Franklin Lakes, NJ, United States) from the jugular vein of Meriz goats (1 male and 1 female) from the flocks of animal project, College of Agricultural Engineering Sciences, University of Duhok, Duhok (geographic coordinates, latitude 36.8679 and longitude, 42.9488), Iraq. Total genomic DNA was isolated from whole blood using the Wizard Genomic DNA Purification kit (Promega, Southampton, UK).

 

Sequencing and assembly of complete mitogenomes

Two samples of genomic DNA of Meriz goats (male and female) (Table 1) were sequenced commercially using Illumina HiSeq-PE150 reads by Novogene Company Limited, Hong Kong, China. Approximately 70-76 million reads of total sequence were given for each genomic DNA sample (Table 1). For each DNA sample, paired end reads were mapped against the complete mitochondrial genome of domestic Dazu black goat (GenBank: KP271023; Guang-Xin et al. 2016) as a reference. After assembling, the two complete mitogenomes of Meriz goats were then annotated. Geneious 8.0 software (Kearse et al. 2012; http://www.geneious.com) was used for bioinformatics analysis (setting paired end reads, mapping and annotation). The annotated complete mitogenomes are available in GenBank under accession numbers MH165338 and MH165339.

 

Data analysis and phylogenetic relationships

To build a phylogenetic tree, the two complete mitogenomes of Meriz goats were aligned with published mitogenomes from domestic and wild goat species representing the six maternal haplogroups _HPGA, _HPGB, _HPGC, _HPGD, _HPGF, and _HPGG (Table 2). To find the best model of mitochondrial sequence alignments, MEGA X (Kumar et al. 2018) was used with setting the maximum likelihood criteria. Thereafter, the phylogenetic position of the assembled mitogenomes of Meriz goats was established by building a phylogenetic tree with the Tamura-Nei (genetic distance model) and neighbour-joining (NJ) method of 1000 bootstrap replicates using Geneious software (Kearse et al. 2012; http://www.geneious.com). The mitogenome of Capra ibex (NCBI ID: FJ207526) was used as out-group.

 

Estimation of mitogenomic diversity

Following multiple alignments of the whole sequences of the mitogenome, the mtDNA sequences were analyzed for nucleotide diversity and polymorphic sites. Evolutionary distances between sequences were estimated by calculating the proportion of nucleotide differences (pairwise differences) between each pair of sequences using MEGA X (Kumar et al. 2018). Additionally, variable sites (polymorphic sites) were calculated using Geneious software (Kearse et al. 2012). The results of nucleotide differences and variable sites were merged together and illustrated in Tables 3 and 4.

 

Table 1 Morphological traits, maternal haplogroups, GenBank accession numbers, mitogenome size, total next generation sequencing (NGS) data and assembled reads of Meriz goats (male and female) using Illumina HiSeq-PE150 reads of total genomic DNA

¹ Haplogroups were identified based on the phylogenetic relation using known haplogroups see Figure 3 and Table 2.

² Total NGS reads= total next generation sequencing raw reads used from each sample.

³ Assembled reads (n)= numbers of assembled NGS raw reads out of total numbers to produce whole mitogenome.

⁴ Coverage= number of assembled reads × 150 [average read length] / mitogenome size.

 

Table 2 Different breeds of domestic and wild goats, their geographical locations, GenBank accession numbers, maternal haplogroups and references used for analysis of phylogenetic tree as shown in Figure 3

 

Table 3 Nucleotide differences (pairwise differences) and variable sites (polymorphic sites) between mitogenome of Meriz goats and and other domestic goat breeds within the same maternal haplogroup (HPGA)

 

Table 4 Nucleotide differences (pairwise differences) and variable sites (polymorphic sites) between mitogenome of Meriz goats and other domestic and wild goat breeds from other maternal haplogroups (HPGB, HPGC, HPGD, HPGF, and HP)

 

RESULTS AND DISCUSSION

Previous research (Huang et al. 2015) used 22 sets of primers to amplify overlapping segments of the mitogenome from different goat breeds. However, in our study, we used next-generation sequencing (NGS) data to sequence the complete mitogenome of Meriz goats. The blood DNA used in this study was appropriate to generate for whole genome sequencing data and to identify whole mitogenomes. As a result of alignment of the 71796930 and 76632598 million NGS raw reads against a reference complete mitogenome of Dazu black goat (GenBank: KP271023), in total 27767 (250X coverage) and 31800 (287X coverage) of raw reads were assembled and circular DNA molecules of the complete mitogenome of the two individuals of Meriz goat with a length of 16641bp (MH165338; male) and 16639 bp (MH165339; female) were produced, respectively (Table 1 and Figures 1 and 2). Likewise, the complete mitogenomes of the Karadi, Hamdani, and Awassi sheep breeds from Iraq were assembled using whole genome sequencing data (Mustafa et al. 2018; Mustafa, 2021).

 

Figure 1 Meriz goat mitogenome map. The assembled mitogenome Capra hircus, Meriz_goat_CHM (16,641 bp) (GenBank accession number MH165338) with major features: 13 protein-coding genes (PCGs) (green bars, with the arrow pointing in the transcription directions), 22 transfer RNA tRNA genes (black triangles), the 12S and 16S rRNA genes (red colour) and the D-loop control region (blue). The GC content is 39.2%. For assembly data, see Table 1

 

The complete record of both mitogenomes of Meriz goats, including gene features (start and stop codons) and other characteristics such as position, sizes and strand distribution of all 13 protein- coding genes (PCGs), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes, and non-coding control region are available under the NCBI accession numbers (MH165338 and MH165339). Typical of mammalian mitochondrial genomes with the AT percentages 60.8% was formed. Ten genes in protein-coding regions begin with the ATG (Met) codon, while ND2, ND3 and ND5 genes use the alternative ATA start codon. Our results are consistent with the structure and distribution of the mitogenome of other vertebrates as reported in previous research (Mustafa et al. 2018 (sheep); Peng et al. 2018 (chicken); De et al. 2019 (cattle); Li et al. 2019 (fish); Xu et al. 2019 (cat)). Moreover, as shown in Table 1, the number of assembled reads (coverage) of the mitogenome is higher in the female Meriz goat in comparison with the male individual. This indicates that the blood cells of female goats have a higher copy number of mitochondria. Similar results were found by Mustafa et al. 2018, in which female sheep were shown to have more copy numbers of mitochondria. In mammalian cells, mitochondria are the key spots of energy production in which their abundance differs according to the organ, age, and physiological condition, such as lactation in female animals (Laubenthal et al. 2016). The phylogenetic position of the assembled mitogenomes of Meriz goats was established by building a phylogenetic tree with the Tamura-Nei (genetic distance model) and neighbour-joining (NJ) method of 1000 bootstrap replicates including published maternal haplogroups of domestic and wild goats (Figure 3 and Table 2). The mitogenome sequences of Meriz goat were positioned on branches with the most predominant maternal haplogroup A (_HPGA) in goats worldwide (Figure 3).

 

Figure 2 Meriz goat mitogenome map. The assembled mitogenome Capra hircus, Meriz_goat_CHF (16,639 bp) (GenBank accession number MH165339) with major features: 13 protein-coding genes (PCGs) (green bars, with the arrow pointing in the transcription directions), 22 transfer RNA tRNA genes (black triangles), the 12S and 16S rRNA genes (red colour) and the D-loop control region (blue). The GC content is 39.2%. For assembly data, see Table 1

 

Meriz goats from Iraq, near the center of diversity and domestication of animal species, are characterized by having the most abundant maternal lineages within the known mitogenomic diversity. The maternal haplogroup of Meriz goats sampled in our study fitted within the main Capra hircus maternal haplogroups known to be present in different goat breeds from Asia and Europe. Previous studies indicated that the most common maternal haplogroup of most goat breeds worldwide was HPGA. For example, the maternal haplogroup HPGA was predominant and widely distributed in Chinese domestic goats (Zhao et al. 2014); Arabian goats in Arab countries (Al-Araimi et al. 2017); Ethiopian goats (Tarekegn et al. 2018); Indian goats (Diwedi et al. 2020); Russian goats (Deniskova et al. 2020); Mongolian goats (Ganbold et al. 2020) and Nepalese goats (Gorkhali et al. 2021). In agreement with the genetic landscape of maternal origin, it can be concluded from the previous studies that the most abundant haplogroup is _HPGA as seen in the most goats worldwide including Meriz goats from Iraq.Colli et al. (2015) suggested in their extensive survey about goat mitogenomes that all modern haplotypes within the haplogroup _HPGA are possibly derived from a single female of wild goats (Capra aegagrus). Results presented here fill a gap of the previous goat samples in geographical coverage of other countries worldwide identifying multiple haplogroups of maternal lineages of goat _HPGA, _HPGB, _HPGC, _HPGD, _HPGF, and , _HPGG (Naderi et al. 2007; Colli et al. 2015). After the mitogenome of Meriz goats was clustered within the maternal haplogroup A, further genetic analysis was performed based on the estimation of nucleotide diversity and polymorphic sites between the mitogenome of Meriz goats and domestic and wild goats of all maternal haplogroups (Table 3 and Table 4).

 

Figure 3 Phylogenetic relationships of Meriz goat mitogenomes. Neighbor-Joining consensus tree showing position of Meriz goats in relation to major haplogroups of domestic goats (Capra hircus) and wild goats (Capra aegagrus). The tree was derived from genetic distance model (Tamura-Nei) analysis of alignments of the whole mitochondrial genome sequences. Nodes are labelled with consensus support %. Scale range (0.005) and line weight (2) were set. The mitogenome of Capra ibex was used as out-group. Table 2 gives accession numbers, place of collection, haplogroups and references for mitogenome sequences used in the tree

 

The overall value of nucleotide differences (pairwise differences) between Meriz goats and other goat breeds within the same clade of haplogroup _HPGA was ranged from 0.0012 to 0.0024 and polymorphic sites were about 21 to 48 (Table 3). However, high variation was found between mitogenome of Meriz goats and domestic and wild goats from other haplogroups _HPGB, _HPGC, _HPGD, _HPGF, and _HPGG (Table 4). Interestingly, the results of phylogeny and nucleotide differences observed the close genetic distances between Meriz goats and Chinese Cashmere producing goats and Turkish Angora goat (Table 3 and Figure 3). However, in comparison to Iranian Marghoz goats, Seyedabadi et al. (2016) analyzed the mitochondrial control region and indicated that all sampled Marghoz goats were classified into maternal haplogroup HPGC. Although both Iraqi Meriz goats and Iranian Markhoz goats have high similarity in terms of phenotype traits and they are present in different morphological colors within Cashmere producing goats (Rashidi et al. 2008; Muhammad Salih Al-Barzinj et al. 2016), their genetic distance in terms of mtDNA sequences is high as each one belongs to a different maternal haplogroup. As indicated in Table 4, the genetic distance between mitogenome of Meriz goats (_HPGA) and mitogenomes of goats from _HPGC was about (0.00977 to 0.01014 pairwise differences and 163 to 169 variable sites). Srirattana et al. (2017) concluded that the mtDNA profiles are not always related to the phenotype in cattle. This could be the same case as we found in Meriz goats in comparison to Iranian Marghoz goats, Chinese Cashmere goats and Turkish Angora goats.

 

CONCLUSION

Phylogenetic analysis of Meriz goats sampled from the center of domestication and diversity of animal species showed they had the most widespread, geographically ubiquitous, maternal haplogroup A (HPGA), one of the six major haplogroups of domestic goats. Nucleotide diversity indicated that Meriz goats have a high level of mitogenomic similarity to Cashmere-producing goats within HPGA, while they are more distant from the rest of the maternal haplogroups. Furthermore, bioinformatics analysis revealed that female goats have more copies of the mitogenome than males. The molecular data described here provides useful knowledge of evolutionary relationships, phylogenetic status and genetic biodiversity of the Meriz goats in the context of breeding and conservation of domestic and wild goats worldwide.

 

ACKNOWLEDGEMENT

We would like to thank the Research Center at the University of Duhok, Iraq letting us use their laboratory facilities for DNA isolation.

 

DATA AVAILABILITY

The annotated mitochondrial DNA sequences are available in GenBank of the NCBI database under accession numbers MH165338 and MH165339. The NGS raw reads that support the results of this study are published in the NCBI database under the BioProject accession number PRJNA797579.

مراجع

Achilli A., BonFigurelio S., Olivieri A., Malusa A., Pala M., Kashani B.H., Perego U.A., Ajmone-Marsan P., Liotta L., Semino O. and Bandelt H.J. (2009). The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PloS One. 4, e5753.

Al-Araimi N.A., Al-Atiyat R.M., Gaafar O.M., Vasconcelos R., Luzuriaga-Neira A., Eisa M.O., Amir N., Benaissa M.H., Alfaris A.A., Aljumaah R.S. and Elnakhla S.M. (2017). Maternal genetic diversity and phylogeography of native Arabian goats. Livest. Sci. 206, 88-94.

Alkass J.E. and Juma K.H. (2005). Small ruminant breeds of Iraq. Pp. 63-101 in Characterization of Small Ruminant Breeds in West Asia and North Africa. L. Iniguez, Ed. International Center for Agriculture Research in the Dry Areas, West Asia. Aleppo, Syria.

Amills M., Capote J. and Tosser‐Klopp G. (2017). Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim. Genet. 48, 631-644.

Colli L., Lancioni H., Cardinali I., Olivieri A., Capodiferro M.R., Pellecchia M., Rzepus M., Zamani W., Naderi S., Gandini F. and Vahidi S.M.F. (2015). Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics. 16, 1-12.

Daly K.G., Delser P.M., Mullin V.E., Scheu A., Mattiangeli V., Teasdale M.D., Hare A.J., Burger J., Verdugo M.P., Collins M.J. and Kehati R. (2018). Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science. 361, 85-88.

De A.K., Muthiyan R., George Z., Ponraj P., Malakar D., Kundu A., Sunder J. and Bhattacharya D. (2019). Complete mitochondrial genome of Trinket cattle, a Danish colonial leftover. Mitochondrial DNA Part B. 4, 2053-2054.

Deniskova T., Bakoev N., Dotsev A., Selionova M. and Zinovieva N. (2020). Maternal origins and haplotype diversity of seven Russian goat populations based on the D-loop sequence variability. Animals. 10, 1603-1611.

Diwedi J., Singh A.W., Ahlawat S., Sharma R., Arora R., Sharma H., Raja K.N., Verma N.K. and Tantia M.S. (2020). Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats. Gene. 756, 144910-144919.

FAO (2000). Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.

Ganbold O., Lee S.H., Paek W.K., Munkhbayar M., Seo D., Manjula P., Khujuu T., Purevee E. and Lee J.H. (2020). Mitochondrial DNA variation and phylogeography of native Mongolian goats. Asian-Australasian J. Anim. Sci. 33, 902-911.

Gorkhali N.A., Lin J., Sapkota S., Pokhrel B.R., Ma Y.H. and Han J.L. (2021). Origin and Genetic Diversity of Nepalese Indigenous Goats (Capra hircus). Agric. Sci. Dig. 2021, 5-11.

Guang-Xin E., Yong-Fu H., Narisu N., Hui-Jiang G., Zhong-Quan Z., Cao-De J., Jia-Hua Z., Yue-Hui M., Li-Peng C., Yan Z., Ya-Wang S. and Yong-Ju Z. (2016). A complete mitochondrial genome of Dazu Black goat. Mitochondrial DNA Part A. 27, 3171-3172.

Harley E.H., de Waal M., Murray S. and O’Ryan C. (2016). Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions. Conserv. Genet. 17, 1285-1291.

Hassanin A., Ropiquet A., Couloux A. and Cruaud C. (2009). Evolution of the mitochondrial genome in mammals living at high altitude: New insights from a study of the tribe Caprini (Bovidae, Antilopinae). J. Mol. Evol. 68, 293-310.

Huang Y., Liu N., Zhao Y., He J., Na R., Zhao Z., Jiang C., Zhang J., Ma Y., Chen L. and Qiu X. (2015). Characteristics of the mitochondrial genome of four native goats in China (Capra hircus). Mitochondrial DNA Part A. 27, 3308-3309.

Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C. and Thierer T. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28, 1647-1649.

Kumar S., Stecher G., Li M., Knyaz C. and Tamura K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547-1549.

Laubenthal L., Hoelker M., Frahm J., Dänicke S., Gerlach K., Südekum K.H., Sauerwein H. and Häussler S. (2016). Mitochondrial DNA copy number and biogenesis in different tissues of early-and late-lactating dairy cows. J. Dairy Sci. 99, 1571-1583.

Li Y.Y., Liu L.X., Sui Z.H., Ma C. and Liu Y.G. (2019). The complete mitochondrial DNA sequence of Mongolian grayling Thymallus brevirostris. Mitochondrial DNA Part B. 4, 1204-1205.

Lippold S., Matzke N.J., Reissmann M. and Hofreiter M. (2011). Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol. Biol. 11, 1-10.

Liu R., Jin L., Long K., Tang Q., Ma J., Wang X., Zhu L., Jiang A.A., Tang G., Jiang Y. and Li X. (2018). Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives. Mitochondrial DNA Part B. 3, 847-851.

Lv F.H., Peng W.F., Yang J., Zhao Y.X., Li W.R., Liu M.J., Ma Y.H., Zhao Q.J., Yang G.L., Wang F. and Li J.Q. (2015). Mitogenomic meta-analysis identifies two phases of migration in the history of eastern Eurasian sheep. Mol. Biol. Evol. 32, 2515-2533.

Ma Y., Su R., Fan Y., Qiao X., Li X., Zhang L. and Li J. (2018). The complete mitochondrial DNA analyses of Inner Mongolia Cashmere goat type of Erlangshan species. Mitochondrial DNA Part B. 3, 44-45.

Mannen H., Yonezawa T., Murata K., Noda A., Kawaguchi F., Sasazaki S., Olivieri A., Achilli A. and Torroni A. (2020). Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci. Rep. 10, 1-7.

Meadows J.R., Cemal I., Karaca O., Gootwine E. and Kijas J.W. (2007). Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics. 175, 1371-1379.

Muhammad Salih Al-Barzinj Y., Asmat Oramari R. and Abdulghany Al-Sanjury R. (2016). Molecular characterization of Iraqi local goat breeds using random amplified polymorphicDNA Marestic goats by large-scale mitochondrial DNA markers. Iranian J. Appl. Anim. Sci. 6, 671-678.

Mustafa S.I., Schwarzacher T. and Heslop-Harrison J.S. (2018). Complete mitogenomes from Kurdistani sheep: Abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA Part A. 29, 1180-1193.‏

Mustafa S.I. (2021). The complete mitogenome of the Iraqi Awassi sheep breed and the maternal lineage utilizing high throughput sequencing raw reads. J. Bangladesh Agric. Univ. 19, 465-470.

Naderi S., Rezaei H.R., Pompanon F., Blum M.G., Negrini R., Naghash H.R., Balkız Ö., Mashkour M., Gaggiotti O.E., Ajmone-Marsan P. and Kence A. (2008). The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl. Acad Sci. 105, 17659-17664.

Naderi S., Rezaei H.R., Taberlet P., Zundel S., Rafat S.A., Naghash H.R., El-Barody M.A., Ertugrul O., Pompanon F. and Econogene C. (2007). Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One. 2, e1012.

Osman S.A.M., Nishibori M. and Yonezawa T. (2021). Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens. Anim. Biosci. 34, 941-948.

Peng S.M., Lin Q., Jiang G.T., Li Y.H., Dai Q.Z., He X. and Yan H.F. (2018). The complete mitochondrial genome of the Dongan black chicken and its phylogenetic analyses. Mitochondrial DNA Part B. 3, 1127-1128.

Rashidi A., Sheikahmadi M., Rostamzadeh J. and Shrestha J.N.B. (2008). Genetic and phenotypic parameter estimates of body weight at different ages and yearling fleece weight in Markhoz goats. Asian-Australasian J. Anim. Sci. 21, 1395-1403.

Seki Y., Yokohama M., Wada K., Fujita M., Kotani M., Nagura Y., Kanno M., Nomura K., Amano T. and Kikkawa Y. (2011). Expression analysis of the type I keratin protein keratin 33A in goat coat hair. Anim. Sci. J. 82, 773-781.

Seyedabadi H.R., Pahlevan Afshari K. and Abdolmaleki M. (2016). Mitochondrial diversity and phylogenetic structure of Marghoz goat population. Iranian J. Appl. Anim. Sci. 6, 679-684.

Shakyawar D.B., Raja A.S.M., Kumar A., Pareek P.K. and Wani S.A. (2013). Pashmina fibre-production, characteristics and utilization. Indian J. Fibre Textile Res. 38, 207-214.

Srirattana K., McCosker K., Schatz T. and John J.C.S. (2017). Cattle phenotypes can disguise their maternal ancestry. BMC Genetics. 18, 1-11.

Tarekegn G.M., Tesfaye K., Mwai O.A., Djikeng A., Dessie T., Birungi J., Osama S., Zergaw N., Alemu A., Achieng G. and Tutah J. (2018). Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecol. Evol. 8, 1543-1553.

Tillmar A.O., Dell'Amico B., Welander J. and Holmlund G. (2013). A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures. PLoS One. 8, e83761.

Wang Z., Wang R., Zhang W., Wang Z., Wang P., Liu H., Gao L., Bai K., Meng R., Zhou J. and Zhang Y. (2013). Estimation of genetic parameters for fleece traits in yearling Inner Mongolia Cashmere goats. Small Rumin. Res. 109, 15-21.

Xu Y., Liu J., Jiang E., Xu Y., Ning F., Du Z. and Bai X. (2019). The complete mitochondrial genome of Pallas's cat (Otocolobus manul). Mitochondrial DNA Part B. 4, 658-659.

Yang L., Tan Z., Wang D., Xue L., Guan M.X., Huang T. and Li R. (2014). Species identification through mitochondrial rRNA genetic analysis. Sci. Rep. 4, 1-11.

Zeder M.A. (2008). Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proc. Natl. Acad. Sci. 105, 11597-11604.

Zhao Y., Zhao R., Zhao Z., Xu H., Zhao E. and Zhang J. (2014). Genetic diversity and molecular phylogeography of Chinese dom. Biol. Rep. 41, 3695-3704.