scholarly journals Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Engel ◽  
Doreen Becker ◽  
Thomas Nissen ◽  
Ingolf Russ ◽  
Georg Thaller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
De Novo ◽  
Breeding Population ◽  
Nucleotide Sequences ◽  
Common Ancestry ◽  
Coding Region ◽  
Horse Breed ◽  
Pairwise Differences

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.

scholarly journals Loss of Genetic Diversity with Captive Breeding and Re-Introduction: A Case Study on Pateke/Brown Teal (Anas chlorotis)

2021 ◽  
Author(s):  
◽  
Gemma Bowker-Wright
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Captive Breeding ◽  
Barrier Island ◽  
Breeding Population ◽  
Island Population ◽  
Wildlife Sanctuary ◽  
Management Options ◽  
Introduced Populations ◽  
Loss Of Genetic Diversity

<p>Pateke/brown teal (Anas chlorotis) have experienced a severe population crash leaving only two remnant wild populations (at Great Barrier Island and Mimiwhangata, Northland). Recovery attempts over the last 35 years have focused on an intensive captive breeding programme which breeds pateke, sourced almost exclusively from Great Barrier Island, for release to establish re-introduced populations in areas occupied in the past. While this important conservation measure may have increased pateke numbers, it was unclear how much of their genetic diversity was being retained. The goal of this study was to determine current levels of genetic variation in the remnant, captive and re-introduced pateke populations using two types of molecular marker, mitochondrial DNA (mtDNA) and microsatellite DNA. Feathers were collected from pateke at Great Barrier Island, Mimiwhangata, the captive breeding population and four re-introduced populations (at Moehau, Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island). DNA was extracted from the base of the feathers, the mitochondrial DNA control region was sequenced, and DNA microsatellite markers were used to genotype individuals. The Great Barrier Island population was found to have only two haplotypes, one in very high abundance which may indicate that historically this population was very small. The captive breeding population and all four re-introduced populations were found to contain only the abundant Great Barrier Island haplotype as the vast majority of captive founders were sourced from this location. In contrast, the Mimiwhangata population contained genetic diversity and 11 haplotypes were found, including the Great Barrier Island haplotype which may have been introduced by captive-bred releases which occurred until the early 1990s. From the microsatellite results, a loss of genetic diversity (measured as average alleles per locus, heterozygosity and allelic richness) was found from Great Barrier Island to captivity and from captivity to re-introduction. Overall genetic diversity within the re-introduced populations (particularly the smaller re-introduced populations at Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island) was much reduced compared with the remnant populations, most probably as a result of small release numbers and small population size. Such loss of genetic diversity could render the re-introduced populations more susceptible to inbreeding depression in the future. Suggested future genetic management options are included which aim for a broader representation of genetic diversity in the pateke captive breeding and release programme.</p>

scholarly journals Loss of Genetic Diversity with Captive Breeding and Re-Introduction: A Case Study on Pateke/Brown Teal (Anas chlorotis)

2021 ◽  
Author(s):  
◽  
Gemma Bowker-Wright
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Captive Breeding ◽  
Barrier Island ◽  
Breeding Population ◽  
Island Population ◽  
Wildlife Sanctuary ◽  
Management Options ◽  
Introduced Populations ◽  
Loss Of Genetic Diversity

<p>Pateke/brown teal (Anas chlorotis) have experienced a severe population crash leaving only two remnant wild populations (at Great Barrier Island and Mimiwhangata, Northland). Recovery attempts over the last 35 years have focused on an intensive captive breeding programme which breeds pateke, sourced almost exclusively from Great Barrier Island, for release to establish re-introduced populations in areas occupied in the past. While this important conservation measure may have increased pateke numbers, it was unclear how much of their genetic diversity was being retained. The goal of this study was to determine current levels of genetic variation in the remnant, captive and re-introduced pateke populations using two types of molecular marker, mitochondrial DNA (mtDNA) and microsatellite DNA. Feathers were collected from pateke at Great Barrier Island, Mimiwhangata, the captive breeding population and four re-introduced populations (at Moehau, Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island). DNA was extracted from the base of the feathers, the mitochondrial DNA control region was sequenced, and DNA microsatellite markers were used to genotype individuals. The Great Barrier Island population was found to have only two haplotypes, one in very high abundance which may indicate that historically this population was very small. The captive breeding population and all four re-introduced populations were found to contain only the abundant Great Barrier Island haplotype as the vast majority of captive founders were sourced from this location. In contrast, the Mimiwhangata population contained genetic diversity and 11 haplotypes were found, including the Great Barrier Island haplotype which may have been introduced by captive-bred releases which occurred until the early 1990s. From the microsatellite results, a loss of genetic diversity (measured as average alleles per locus, heterozygosity and allelic richness) was found from Great Barrier Island to captivity and from captivity to re-introduction. Overall genetic diversity within the re-introduced populations (particularly the smaller re-introduced populations at Karori Wildlife Sanctuary, Tiritiri Matangi Island and Mana Island) was much reduced compared with the remnant populations, most probably as a result of small release numbers and small population size. Such loss of genetic diversity could render the re-introduced populations more susceptible to inbreeding depression in the future. Suggested future genetic management options are included which aim for a broader representation of genetic diversity in the pateke captive breeding and release programme.</p>

scholarly journals Strategies and difficulties in assembling highly recombinogenic plant organelle genomes: a case study

2015 ◽  
Author(s):  
Concita Cantarella ◽  
Rachele Tamburino ◽  
Nunzia Scotti ◽  
Teodoro Cardi ◽  
Nunzio D'Agostino
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
De Novo ◽  
Sequence Data ◽  
Repeated Sequences ◽  
Read Length ◽  
Plant Mitochondrial Genome ◽  
Sequencing Platform ◽  
Organelle Genomes ◽  
Long Read

Mitochondrial genomes in plants are larger and more complex than in other eukaryotes due to their recombinogenic nature as widely demonstrated. The mitochondrial DNA (mtDNA) is usually represented as a single circular map, the so-called master molecule. This molecule includes repeated sequences, some of which are able to recombine, generating sub-genomic molecules in various amounts, depending on the balance between their recombination and replication rates. Recent advances in DNA sequencing technology gave a huge boost to plant mitochondrial genome projects. Conventional approaches to mitochondrial genome sequencing involve extraction and enrichment of mitochondrial DNA, cloning, and sequencing. Large repeats and the dynamic mitochondrial genome organization complicate de novo sequence assembly from short reads. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality (fewer gaps and longer contigs). However, recently published articles revealed that PacBio sequencing is still not sufficient to address mtDNA assembly-related issues. Here we present a preliminary hybrid assembly of a potato mtDNA based on both PacBio and Illumina reads and debate the strategies and obstacles in assembling genomes containing repeated sequences that are recombinationally active and serve as a constant source of rearrangements.

scholarly journals Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations.

Genetics ◽  
1988 ◽  
Vol 118 (4) ◽  
pp. 649-663
Author(s):  
R Garesse
Keyword(s):  
Mitochondrial Dna ◽  
Drosophila Melanogaster ◽  
Mitochondrial Genome ◽  
Gene Organization ◽  
Coding Region ◽  
Similar Frequency ◽  
Predominant Type ◽  
Drosophila Yakuba ◽  
Very High ◽  
Type Of Transition

Abstract The sequence of a 8351-nucleotide mitochondrial DNA (mtDNA) fragment has been obtained extending the knowledge of the Drosophila melanogaster mitochondrial genome to 90% of its coding region. The sequence encodes seven polypeptides, 12 tRNAs and the 3' end of the 16S rRNA and CO III genes. The gene organization is strictly conserved with respect to the Drosophila yakuba mitochondrial genome, and different from that found in mammals and Xenopus. The high A + T content of D. melanogaster mitochondrial DNA is reflected in a reiterative codon usage, with more than 90% of the codons ending in T or A, G + C rich codons being practically absent. The average level of homology between the D. melanogaster and D. yakuba sequences is very high (roughly 94%), although insertion and deletions have been detected in protein, tRNA and large ribosomal genes. The analysis of nucleotide changes reveals a similar frequency for transitions and transversions, and reflects a strong bias against G + C on both strands. The predominant type of transition is strand specific.

scholarly journals Characterisation of the Mitochondrial Genome and the Population Genetics of Polyprion Oxygeneios (Hapuku) from Around New Zealand

2021 ◽  
Author(s):  
◽  
Henry Somerset Lane
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Population Genetic Structure ◽  
Microsatellite Dna ◽  
Population Genetic ◽  
The West ◽  
Polyprion Oxygeneios

<p><b>Polyprion oxygeneios (hapuku) is an important commercial and recreational fishery species within New Zealand. Moreover, P. oxygeneios are currently being developed as a high-value New Zealand aquaculture species. There have been no previous studies on New Zealand’s P. oxygeneios that have been able to detect genetic differences among samples, which may be of use to either broodstock or fisheries managers. An understanding of the genetic structure of commercially harvested species maximises the potential for sustainable harvesting through effective management schemes. The primary goal of this thesis was to investigate the population genetic structure of P. oxygeneios using molecular markers to analyse samples collected from sites within New Zealand’s Exclusive Economic Zone (EEZ).</b></p> <p>The DNA sequence of the whole mitochondrial genome of P. oxygeneios was determined and it showed a similar structure and gene organisation to that of other species across a wide range of taxa. A set of species-specific control region primers was developed for P. oxygeneios and Polyprion americanus, and additional primers were designed for the 16S and ND6 genes of P. oxygeneios. A ~488 bp portion of the mitochondrial DNA (mtDNA) control region sequence from 274 individuals, and genotypes from 259 individuals using nine polymorphic microsatellite loci, were used to investigate the phylogeography and population genetic structure of P. oxygeneios. The mitochondrial DNA data failed to detect any significant differentiation between sample sites. However, the microsatellite DNA analyses showed that individuals sampled from the west coast of the South Island (Hokitika) were genetically distinct from individuals sampled at all other New Zealand sites. These two groups might be representative of two discrete populations of P. oxygeneios within New Zealand’s EEZ. These results suggest that the west coast South Island P. oxygeneios fishery should continue to be managed as a separate stock, with some possible revision of the Cook Strait fishery required. Analyses of the mtDNA and microsatellite DNA data of P. oxygeneios broodstock held at NIWA’s Bream Bay Aquaculture Park showed that they were not significantly differentiated from the wild populations (excluding Hokitika). Simulations also described the appropriate sampling efforts required to capture an appropriate level of genetic diversity when either establishing a new broodstock or supplementing an existing broodstock with new individuals. Continued management of the broodstock will be required to maintain the high levels of genetic diversity that have been captured in the founding broodstock in future generations.</p>

scholarly journals Characterisation of the Mitochondrial Genome and the Population Genetics of Polyprion Oxygeneios (Hapuku) from Around New Zealand

2021 ◽  
Author(s):  
◽  
Henry Somerset Lane
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Population Genetic Structure ◽  
Microsatellite Dna ◽  
Population Genetic ◽  
The West ◽  
Polyprion Oxygeneios

<p><b>Polyprion oxygeneios (hapuku) is an important commercial and recreational fishery species within New Zealand. Moreover, P. oxygeneios are currently being developed as a high-value New Zealand aquaculture species. There have been no previous studies on New Zealand’s P. oxygeneios that have been able to detect genetic differences among samples, which may be of use to either broodstock or fisheries managers. An understanding of the genetic structure of commercially harvested species maximises the potential for sustainable harvesting through effective management schemes. The primary goal of this thesis was to investigate the population genetic structure of P. oxygeneios using molecular markers to analyse samples collected from sites within New Zealand’s Exclusive Economic Zone (EEZ).</b></p> <p>The DNA sequence of the whole mitochondrial genome of P. oxygeneios was determined and it showed a similar structure and gene organisation to that of other species across a wide range of taxa. A set of species-specific control region primers was developed for P. oxygeneios and Polyprion americanus, and additional primers were designed for the 16S and ND6 genes of P. oxygeneios. A ~488 bp portion of the mitochondrial DNA (mtDNA) control region sequence from 274 individuals, and genotypes from 259 individuals using nine polymorphic microsatellite loci, were used to investigate the phylogeography and population genetic structure of P. oxygeneios. The mitochondrial DNA data failed to detect any significant differentiation between sample sites. However, the microsatellite DNA analyses showed that individuals sampled from the west coast of the South Island (Hokitika) were genetically distinct from individuals sampled at all other New Zealand sites. These two groups might be representative of two discrete populations of P. oxygeneios within New Zealand’s EEZ. These results suggest that the west coast South Island P. oxygeneios fishery should continue to be managed as a separate stock, with some possible revision of the Cook Strait fishery required. Analyses of the mtDNA and microsatellite DNA data of P. oxygeneios broodstock held at NIWA’s Bream Bay Aquaculture Park showed that they were not significantly differentiated from the wild populations (excluding Hokitika). Simulations also described the appropriate sampling efforts required to capture an appropriate level of genetic diversity when either establishing a new broodstock or supplementing an existing broodstock with new individuals. Continued management of the broodstock will be required to maintain the high levels of genetic diversity that have been captured in the founding broodstock in future generations.</p>

scholarly journals Strategies and difficulties in assembling highly recombinogenic plant organelle genomes: a case study

2015 ◽  
Author(s):  
Concita Cantarella ◽  
Rachele Tamburino ◽  
Nunzia Scotti ◽  
Teodoro Cardi ◽  
Nunzio D'Agostino
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
De Novo ◽  
Sequence Data ◽  
Repeated Sequences ◽  
Read Length ◽  
Plant Mitochondrial Genome ◽  
Sequencing Platform ◽  
Organelle Genomes ◽  
Long Read

Mitochondrial genomes in plants are larger and more complex than in other eukaryotes due to their recombinogenic nature as widely demonstrated. The mitochondrial DNA (mtDNA) is usually represented as a single circular map, the so-called master molecule. This molecule includes repeated sequences, some of which are able to recombine, generating sub-genomic molecules in various amounts, depending on the balance between their recombination and replication rates. Recent advances in DNA sequencing technology gave a huge boost to plant mitochondrial genome projects. Conventional approaches to mitochondrial genome sequencing involve extraction and enrichment of mitochondrial DNA, cloning, and sequencing. Large repeats and the dynamic mitochondrial genome organization complicate de novo sequence assembly from short reads. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality (fewer gaps and longer contigs). However, recently published articles revealed that PacBio sequencing is still not sufficient to address mtDNA assembly-related issues. Here we present a preliminary hybrid assembly of a potato mtDNA based on both PacBio and Illumina reads and debate the strategies and obstacles in assembling genomes containing repeated sequences that are recombinationally active and serve as a constant source of rearrangements.

Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA.

Genetics ◽  
1994 ◽  
Vol 137 (1) ◽  
pp. 233-241 ◽  
Author(s):  
D J Stanton ◽  
L L Daehler ◽  
C C Moritz ◽  
W M Brown
Keyword(s):  
Mitochondrial Dna ◽  
De Novo ◽  
Direct Sequence ◽  
Sequence Repeat ◽  
Coding Region ◽  
Gene Encoding ◽  
Mt Dna ◽  
Whiptail Lizards ◽  
Tandem Duplications

Abstract Tandem duplications of gene-encoding regions occur in the mitochondrial DNA (mt DNA) of some individuals belonging to several species of whiptail lizards (genus Cnemidophorus). All or part of the duplicated regions of the mtDNAs from five different species were sequenced. In all, the duplication endpoints were within or immediately adjacent to sequences in tRNA, rRNA or protein genes that are capable of forming energetically stable stem-and-loop structures. In two of these mtDNAs, the duplication endpoints were also associated with a direct sequence repeat of 13 bp. The consistent association of stem-and-loop structures with duplication endpoints suggests that these structures may play a role in the duplication process. These data, combined with the absence of direct or palindromic repeats at three of the pairs of duplication endpoints, also suggest the existence of a mechanism for generating de novo duplications that is qualitatively different from those previously modeled.

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