Complete mitogenomes from Kurdistani sheep – abundant centromeric nuclear copies representing diverse ancestors

Kurdistani sheep breeds and part of their mitochondrial genome From Mustafa et al. Mitochondrial DNA part A 2018.

Kurdistani sheep breeds and part of their mitochondrial genome From Mustafa et al. Mitochondrial DNA part A 2018.

341. Mustafa SI, Schwarzacher T, and Heslop-Harrison JS. 2018. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestorsMitochondrial DNA Part A https://doi.org/10.1080/24701394.2018.1431226 (publisher – see free publisher link below if you can’t access) AND Mustafa et al_2018 AuthorVersion

The geographical center of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the ‘Fertile Crescent’. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.

Keywords: nuclear mitochondrial DNA segments (numts); mitogenome diversity; massively parallel sequencing; fluorescent in situ hybridization; sheep domestication

Free link to paper from publishers: http://www.tandfonline.com/eprint/YSxE33mSJiBMVEuMXIyv/full (limited to 50 uses so please look at author version first or use your academic library link via DOI below!)

341. Mustafa SI, Schwarzacher T, and Heslop-Harrison JS. 2018. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestorsMitochondrial DNA Part A https://doi.org/10.1080/24701394.2018.1431226 () Mustafa et al_2018 AuthorVersion

 

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Morphology, adaptation and speciation

Plant adaptation arises from their morphology, itself a product of evolution and development. In this figure, the aspects and interactions of research at different levels are shown, with the work having implications across botany, including understanding plant phylogeny and speciation, and for ecology and ecosystems.

Plant adaptation arises from their morphology, itself a product of evolution and development. In this figure, the aspects and interactions of research at different levels are shown, with the work having implications across botany, including understanding plant phylogeny and speciation, and for ecology and ecosystems.

Heslop-Harrison JS. 2017. Morphology, adaptation and speciation. Annals of Botany 120(7): 621-624. https://doi.org/10.1093/aob/mcx130The study of plant evolution and development in a phylogenetic context has accelerated research advances in both areas over the last decade. The addition of a robust phylogeny for plant taxa based on DNA as well as morphology has given a strong context for this research. Genetics and genomics, including sequencing of many genes, and a better understanding of non-genetic, responsive changes, by plants have increased knowledge of how the different body forms of plants have arisen. Here, I overview the papers in this Special Issue of Annals of Botany on Morphological Adaptation, bringing together a range of papers that link phylogeny and morphology. These lead to models of development and functional adaptation across a range of plant systems, with implications for ecology and ecosystems, as well as development and evolution.

The study of evolution and development (evo-devo) has advanced plant research including speciation (Fernández-Mazuecos and Glover 2017); and as Theodore Dobzhansky stated in 1973, ‘nothing makes sense except in the light of evolution’. But what options are there for plant architecture to evolve – from the gene to cellular to organ and on to whole plant and ecosystem level? As suggested in the mind-map of Fig. 1, we are now in a good position to exploit data from morphological and genetic studies to understand the key processes of evolution and development, taking those results to find their impact on ecology and ecosystems. The papers in this special issue cover a diverse range of species, organs (related to leaves, roots and flowers) and approaches (from advanced microscopy to DNA fingerprinting), to show how modern plant studies can be integrated to lead to models of evolution and understand plant development in the broadest context.

 

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Crop Improvement – Plant Nuclear Genomes

328. Heslop-Harrison JS. 2017. Crop Improvement: Plant Nuclear Genomes. Encyclopedia of Applied Plant Sciences 2nd Edition. In proof.

Plant breeders work with large amounts of DNA sequence information including the sequences of all genes and the repetitive DNA that makes up the majority of most genomes. Knowledge of the diversity and evolution of the sequences is proving important to developing DNA markers, indentifying genetic and QTL characters, the selection of breeding lines and the measurement and exploitation of biodiversity. Nuclear DNA sequence information can be used for improvement all crop species with directed superdomestication approaches leading to improved performance, resistances to biotic and abiotic stress, and greater environmental sustainability to meet the challenges of increasing populations and climate change.

Keywords

Biodiversity, Breeding, Epigenetics, Genetics, Genomics, Genomes, Repetitive DNA, Traits, Plastomes, Chloroplasts, Markers, QTL, Chromosomes, Genome size

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Repetitive DNA in the catfish genome- rDNA, microsatellites, and Tc1-mariner transposon sequences in Imparfinis

Repetitive sequence organization on chromosomes of a Brazilian catfish species, important for understanding their evolution and biodiversity. Gouveia et al., Journal of Heredity, 2017.

Repetitive sequence organization on chromosomes of a Brazilian catfish species, important for understanding their evolution and biodiversity. Gouveia et al., Journal of Heredity, 2017.

339. Gouveia JG, Wolf IR, Vilas-Boas LA, Heslop-Harrison JS, Schwarzacher T, Dias AL. 2017. Repetitive DNA in the catfish genome: rDNA, microsatellites, and Tc1-mariner transposon sequences in Imparfinis species (Siluriformes, Heptapteridae). Journal of Heredity 108(6): 650-657.

Journal link: https://doi.org/10.1093/jhered/esx065 Author PHHGouveia_CatfishRepeatsAuthorVersion

Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I.  schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I.  schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.

Subject area: Genomics and gene mapping
Key words: genome evolution, karyotype evolution, MITEs, transposable elements

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Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants

337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120(2): 183-194. https://doi.org/10.1093/aob/mcx079  (Free access).

Polyploidy, defined as whole genome duplication, is present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. This Annals of Botany Special Issue on Polyploidy in Ecology and Evolution presents the evolutionary consequences of new, recent, and ancient polyploidy. Alix et al. survey experimental, genomic, ecological and theoretical studies demonstrating that polyploidization often occurs during periods of major evolutionary transitions and adaptive radiation of species. Polyploidy, the cornerstone of bursts of adaptive speciation, brings about genetic novelty. The emergence of new gene functions enables diversification, speciation, and hence plant evolution.

The figure can be downloaded in Powerpoint format here AlixSchwarzacherHeslopHarrisonPlantEvolutionPolyploidyWGDAnnalsBotany format.

Background Polyploidy or whole genome duplication is now recognized as being
present in almost all lineages of higher plants, with multiple rounds of polyploidy
occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridisation events are found in about half of the world’s crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this article, consider genomic aspects of polyploidy.
• Approaches Discovery of the evolutionary consequences of new, evolutionarily
recent, and ancient polyploidy requires a range of approaches. Large scale studies of
both single species, and whole ecosystems, with hundreds to tens of thousands of
individuals, sometimes involving ‘garden’ or transplant experiments are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution, require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.
• Conclusions The success of polyploidy, displacing the diploid ancestors of almost all
plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidisation events. Strikingly, polyploidisation often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting that concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole genome duplication act as a driver of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

Key words: Polyploidy, hybrids, ecology, adaptation, evolution, genomics, chromosomes, speciation, whole genome duplication (WGD), crops, weeds, phylogeny, bryophytes,
angiosperms

Published version: https://doi.org/10.1093/aob/mcx079  (Free access).

And

AlixPolyploidy2017AuthorVersion.

 

Update 16/8/2017 to add author version (although original is free acces) and page reference.

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Identification and characterization of mobile genetic elements LINEs from Brassica genome

Nouroz F, Noreen S, Khan MF, Ahmed S, Heslop-Harrison JS. 2017. Identification and characterization of mobile genetic elements LINEs from Brassica genomes. Gene 627: 94-105. doi: 10.1016/j.gene.2017.06.015..

Abstract
Among transposable elements (TEs), the LTR retrotransposons are abundant followed by nonLTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four nonautonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to ‘R’ and ‘I’ type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were
observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars.

Keywords: Retrotransposons, Brassica, LINEs, Reverse transcriptase, Diversity, Phylogeny.

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Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants

Fig1PolyploidyAlixEtAl.jpg337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120: 183–194. https://dx.doi.org/10.1093/aob/mcx079 (freely available)

Author version (free to post) to come. Figure 1 showing polyploidy or WGD whole genome duplication events in plant evolution is here AlixSchwarzacherHeslopHarrisonPlantEvolutionPolyploidyWGDAnnalsBotany (Powerpoint format)

  • Background. Polyploidy or whole genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridisation events are found in about half of the world’s crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this article, consider genomic aspects of polyploidy.
  • Discovery of the evolutionary consequences of new, evolutionarily recent, and ancient polyploidy requires a range of approaches. Large scale studies of both single species, and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving ‘garden’ or transplant experiments are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution, require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.
  • Conclusions: The success of polyploidy, driving out the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidisation events. Strikingly, polyploidisation often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting that concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole genome duplication act as a driver of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.

 

Keywords: Polyploidy, hybrids, ecology, adaptation, evolution, genomics, chromosomes, speciation, whole genome duplication (WGD), crops, weeds, phylogeny, bryophytes, angiosperms

337. Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS. 2017. Polyploidy and interspecific hybridisation: partners for adaptation, speciation and evolution in plants. Annals of Botany 120: 183–194. https://dx.doi.org/10.1093/aob/mcx079

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