Non-coding RNAs mediate the rearrangements of genomic DNA in ciliates

Most eukaryotes employ a variety of mechanisms to defend the integrity of their genome by recognizing and silencing parasitic mobile nucleic acids. However, recent studies have shown that genomic DNA undergoes extensive rearrangements, including DNA elimination, fragmentation, and unscrambling, during the sexual reproduction of ciliated protozoa. Non-coding RNAs have been identified to program and regulate genome rearrangement events. In Paramecium and Tetrahymena, scan RNAs (scnRNAs) are produced from micronuclei and transported to vegetative macronuclei, in which scnRNA elicits the elimination of cognate genomic DNA. In contrast, Piwi-interacting RNAs (piRNAs) in Oxytricha enable the retention of genomic DNA that exhibits sequence complementarity in macronuclei. An RNA interference (RNAi)-like mechanism has been found to direct these genomic rearrangements. Furthermore, in Oxytricha, maternal RNA templates can guide the unscrambling process of genomic DNA. The non-coding RNA-directed genome rearrangements may have profound evolutionary implications, for example, eliciting the multigenerational inheritance of acquired adaptive traits.     

Comparative Genome Analysis between Agrostis stolonifera and Members of the Pooideae Subfamily,including Brachypodium distachyon

Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.     

Chromosome evolution in malaria mosquitoes

The genomic era offers excellent opportunities to improve our understanding of the genetic basis of mosquito adaptation, evolution, and competence to a pathogen. The availability of polytene chromosomes in anopheline mosquitoes makes them an excellent model system for studying genome organization, evolution, and function. Physical mapping facilitated the whole genome sequence assembly for the major malaria vector Anopheles gambiae and comparative genome mapping has determined types, patterns, and rates of chromosomal rearrangements in mosquito evolution. Together with sequencing projects, high-resolution physical mapping can shed light on mechanisms of chromosomal rearrangements and phylogenetic relation-ships among species.     

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. Here, we examine genomic sequences from closely related fruit fly taxa of the Drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. Partial genomic assemblies were generated from two subspecies of Drosophila pseudoobscura (D. ps.) and an outgroup species, D. miranda. These new assemblies were compared to available assemblies of D. ps. pseudoobscura and D. persimilis, two species with overlapping ranges in western North America. Within inverted regions, nucleotide divergence among each pair of the three species is comparable, whereas divergence between D. ps. pseudoobscura and D. persimilis in non-inverted regions is much lower and closer to levels of intraspecific variation. Using molecular markers flanking each of the major chromosomal inversions, we identify strong crossover suppression in F₁ hybrids extending over 2 megabase pairs (Mbp) beyond the inversion breakpoints. These regions of crossover suppression also exhibit the high nucleotide divergence associated with inverted regions. Finally, by comparison to a geographically isolated subspecies, D. ps. bogotana, our results suggest that autosomal gene exchange between the North American species, D. ps. pseudoobscura and D. persimilis, occurred since the split of the subspecies, likely within the last 200,000 years. We conclude that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization. Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems.     

The shrunken genome of Arabidopsis thaliana

This paper examines macro and micro-level patterns of genome size evolution in the Brassicaceae. A phylogeny of 25 relatives of Arabidopsis thaliana was reconstructed using four molecular markers under both parsimony and Bayesian methods. Reconstruction of genome size (C value) evolution as a discrete character and as a continuous character was also performed. In addition, size dynamics in small chromosomal regions were assessed by comparing genomic clones generated for Arabidopsis lyrata and for Boechera stricta to the fully sequenced genome of A. thaliana. The results reveal a sevenfold variation in genome size among the taxa investigated and that the small genome size of A. thaliana is derived. Our results also indicate that the genome is free to increase or decrease in size across these evolutionary lineages without a directional bias. These changes are accomplished by insertions and deletions at both large and small-scales occurring mostly in intergenic regions, with repetitive sequences and transposable elements implicated in genome size increases. The focus upon taxa relatively closely related to the model organism A. thaliana, and the combination of complementary approaches, allows for unique insights into the processes driving genome size changes.     

Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac (Muntiacus muntjak vaginalis)

The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones selected by chromosome painting for this special muntjac species. Sequence comparison on these BAC clones uncovered sequence syntenic relationships between the muntjac genome and those of other mammals. We found that the muntjac genome has peculiar features with respect to intron size and evolutionary rates of genes. Inspection of more than 80 pairs of orthologous introns from 15 genes reveals a significant reduction in intron size in the Indian muntjac compared to that of human, mouse, and dog. Evolutionary analysis using 19 genes indicates that the muntjac genes have evolved rapidly compared to other mammals. In addition, we identified and characterized sequence composition of the first BAC clone containing a chromosomal fusion site. Our results shed new light on the genome architecture of the Indian muntjac and suggest that chromosomal rearrangements have been accompanied by other salient genomic changes. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.Qi Zhou, Ling Huang, Jianguo Zhang: these authors contributed equally to the paper.Sequence data from this article have been deposited in the GenBank Libraries under Accession No. DQ280153-DQ280188, DQ377335, DQ458964.     

Classification and identification of the Burkholderia cepacia complex: Past, present and future

The Burkholderia cepacia complex is a group of closely related species with conflicting biological properties. Triggered by the devastating effect of pulmonary infections in cystic fibrosis patients, the scientific community generated an unusually large amount of taxonomic data for these bacteria during the past 15 years. This review presents the polyphasic, multilocus and genomic methodology used for the classification and identification of these bacteria. The current state-of-the-art demonstrates that present day taxonomists can replace traditional DNA-DNA hybridizations for species level demarcation and 16S rRNA sequence analysis for studying phylogeny by superior whole genome sequence-based parameters within the framework of polyphasic taxonomic studies.     

Phylogeny and molecular evolution of the Acc1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy gene encoding plastid acetyl-CoA carboxylase (Acc1) within the StH genome species, two Acc1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from 35 diploid taxa representing 19 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) the StH genome species from the same areas or neighboring geographic regions are closely related to each other; (2) the Acc1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) Dasypyrum has contributed to the nuclear genome of Elymus repens and Elymus mutabilis; (4) the StH genome polyploids have higher levels of sequence diversity in the H genome homoeolog than the St genome homoeolog; and (5) the Acc1 sequence may evolve faster in the polyploid species than in the diploids. Our result provides some insight on evolutionary dynamics of duplicate Acc1 gene, the polyploidy speciation and phylogeny of the StH genome species.     

猴樟叶绿体基因组特征分析

猴樟(Cinnamomum bodinieri)枝叶含有丰富的精油,是重要的园林绿化树种和经济树种,但目前有关猴樟基因组学的研究报道不多。为揭示猴樟叶绿体基因组特征及系统发育关系,该文基于高通量测序平台进行测序,从头组装了完整的猴樟叶绿体基因组,并对其基因组结构、基因构成及序列重复、密码子使用偏好性以及系统发育进行分析,结合樟亚科主要属物种叶绿体基因组数据构建系统发育树。结果表明:(1)猴樟叶绿体基因组全长152 727 bp,包括一对20 132 bp的反向重复(IRs)区、93 605 bp的大单拷贝(LSC)区和18 858 bp的小单拷贝(SSC)区,总GC含量为39.13%。(2)该基因组共编码127个基因,包括83个蛋白质编码基因(PCGs)、36个转运RNA基因(tRNAs)和8个核糖体RNA基因(rRNAs); 共鉴定出92个SSR位点,其中大部分是A/T组成的单核苷酸重复序列; 密码子适应指数(CAI)为0.166,有效密码子数(ENc)为54.68; 猴樟与近缘种的叶绿体基因组主要在IR区和2个SC区边界上存在一定的差异。(3)24种樟亚科植物的系统发育树显示,猴樟与樟树亲缘关系最近,同时支持了樟属-甜樟属分支(Cinnamomum-Ocotea Clade)、月桂属-新木姜子属分支(Laurus-Neolitsea Clade)、润楠属-鳄梨属分支(Machilus-Persea Clade)的建立。该研究丰富了猴樟遗传资源信息,进一步确定了樟亚科主要属的系统发育地位。     

Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis

Background

Amycolatopsis orientalis is the type species of the genus and its industrial strain HCCB10007, derived from ATCC 43491, has been used for large-scale production of the vital antibiotic vancomycin. However, to date, neither the complete genomic sequence of this species nor a systemic characterization of the vancomycin biosynthesis cluster (vcm) has been reported. With only the whole genome sequence of Amycolatopsis mediterranei available, additional complete genomes of other species may facilitate intra-generic comparative analysis of the genus.

Results

The complete genome of A. orientalis HCCB10007 comprises an 8,948,591-bp circular chromosome and a 33,499-bp dissociated plasmid. In total, 8,121 protein-coding sequences were predicted, and the species-specific genomic features of A. orientalis were analyzed in comparison with that of A. mediterranei. The common characteristics of Amycolatopsis genomes were revealed via intra- and inter-generic comparative genomic analyses within the domain of actinomycetes, and led directly to the development of sequence-based Amycolatopsis molecular chemotaxonomic characteristics (MCCs). The chromosomal core/quasi-core and non-core configurations of the A. orientalis and the A. mediterranei genome were analyzed reciprocally, with respect to further understanding both the discriminable criteria and the evolutionary implementation. In addition, 26 gene clusters related to secondary metabolism, including the 64-kb vcm cluster, were identified in the genome. Employing a customized PCR-targeting-based mutagenesis system along with the biochemical identification of vancomycin variants produced by the mutants, we were able to experimentally characterize a halogenase, a methyltransferase and two glycosyltransferases encoded in the vcm cluster. The broad substrate spectra characteristics of these modification enzymes were inferred.

Conclusions

This study not only extended the genetic knowledge of the genus Amycolatopsis and the biochemical knowledge of vcm-related post-assembly tailoring enzymes, but also developed methodology useful for in vivo studies in A. orientalis, which has been widely considered as a barrier in this field.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-363) contains supplementary material, which is available to authorized users.     

Clustered organization and conservation of theXiphophorus maculatus D locus,which includes two distinct gene sequences

Genomic organization and chromosomal localization of a previously uncharacterizedD (Donor) locus inXiphophorus andPoecilia species was investigated using fluorescence in situ hybridization (FISH) and Southern blot analysis. Part of this region is thought to be involved in the recombination event leading to formation of theXmrk oncogene and it has recently been shown that this locus included two different genes, one with high homology to a zinc finger protein of the Krüppel type, and the other an unknown gene with high similarity to aCaenorhabditis elegans gene. FISH toXiphophorus chromosomes revealed that these two unrelated genes are closely linked and clustered at a unique chromosomal site. Southern blot hybridization patterns suggest that these genes exist in the genome as multiple copies. Furthermore, similar genomic organization profiles seem to prevail among other related fish. In particular, our FISH experiments reveal the existence of a conserved homologous chromosomal segment harboring the zinc finger protein sequence in several poeciliid fish.     

An improved method of genomic in situ hybridization (GISH) for distinguishing closely related genomes of tetraploid and hexaploid wheat species

An improved modification of genomic in situ hybridization (GISH) was proposed. It allows clear and reproducible discrimination between closely related genomes of both tetraploid and hexaploid wheat species due to preannealing of labeled DNA probes and prehybridization of chromosomal samples with blocking DNA. The method was applied to analyze intergenomic translocations 6A:6B and 1A:6B identified in the IG46147 and IG116188 samples of tetraploid wheat Triticum dicoccoides by C-banding. The structure of the rearranged chromosomes was defined for two translocation variants, and the breakpoints were identified on the chromosome arms. Possible application of the developed GISH variant to study genome reorganizations during speciation of allopolyploid plants in evolution is discussed.     

RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans

Deinococcus radiodurans is one of the most radiation-resistant organisms known. It can repair hundreds of radiation-induced double-strand DNA breaks without loss of viability. Genome reassembly in heavily irradiated D. radiodurans is considered to be an error-free process since no genome rearrangements were detected after post-irradiation repair. Here, we describe for the first time conditions that frequently cause erroneous chromosomal assemblies. Gross chromosomal rearrangements have been detected in recA mutant cells that survived exposure to 5 kGy γ-radiation. The recA mutants are prone also to spontaneous DNA rearrangements during normal exponential growth. Some insertion sequences have been identified as dispersed genomic homology blocks that can mediate DNA rearrangements. Whereas the wild-type D. radiodurans appears to repair accurately its genome shattered by 5 kGy γ-radiation, extremely high γ-doses, e.g., 25 kGy, produce frequent genome rearrangements among survivors. Our results show that the RecA protein is quintessential for the fidelity of repair of both spontaneous and γ-radiation-induced DNA breaks and, consequently, for genome stability in D. radiodurans. The mechanisms of decreased genome stability in the absence of RecA are discussed.     

Correlated evolution of LTR retrotransposons and genome size in the genus <Emphasis Type="Italic">eleocharis</Emphasis>

Background  

Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis.     

红锥叶绿体基因组特征及系统发育分析

为确定红锥(Castanopsis hystrix)叶绿体基因组的结构组成情况,判定其在锥属中的进化位置及与同锥属叶绿体基因组的区别,为锥属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina HiSeq 2500测序平台对红锥叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,并利用R、Python、MISA、CodonW和MEGA 6等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、简单重复序列(simple sequence repeat,SSR)位点和系统发育进行分析。结果表明红锥叶绿体基因组大小为153754 bp,呈现四分体结构;共拥有130个基因,包含85个编码基因、37个tRNA基因和8个rRNA基因;通过密码子偏好性分析,平均有效密码子数为55.5,说明其密码子随机性强、偏好性低;通过SSR及长重复片段分析,检测到45个重复序列及111个SSR位点;与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高;此外,系统发育分析发现红锥与海南锥聚为一支,关系密切。本研究得到了红锥的叶绿体基因组基本情况与系统发育位置,为红锥的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。     

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

Background

By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.

Results

We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.

Conclusions

Our data suggest that adaptive alleles – in this case, genes involved in the immune response – might have been favored by genome rearrangements in the macaque lineage.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-530) contains supplementary material, which is available to authorized users.     

A genomic view of introgression and hybrid speciation

Hybridization in plants and animals is more common and has more complex outcomes than previously realized. Genome-wide analyses of introgression in organisms ranging from oaks to sunflowers to fruit flies show that a substantial fraction of their genomes are permeable to alleles from related species. Hybridization can lead to rapid genomic changes, including chromosomal rearrangements, genome expansion, differential gene expression, and gene silencing, some of which are mediated by transposable elements. These genomic changes may lead to beneficial new phenotypes, and selection for fertility and ecological traits may in turn alter genome structure. Dramatic increases in the availability of genomic tools will produce a new understanding of the genetic nature of species and will resolve a century-old debate over the basis of hybrid vigor, while the natural recombinants found in hybrid zones will permit genetic mapping of species differences and reproductive barriers in nonmodel organisms.     

Cis-acting transmission of genomic instability

Genomic instability is a highly pleiotropic phenotype, which may reflect a variety of underlying mechanisms. Destabilization has been shown in some cases to involve mutational alteration or inactivation of trans-acting cellular factors, for example, p53 or mismatch repair functions. However, aspects of instability are not well explained by mutational inactivation of trans-acting factors, and other epigenetic and cis-acting mechanisms have recently been proposed. The trans and cis models result in divergent predictions for the distribution of instability-associated genetic alterations within the genome, and for the inheritance of genomic instability among sibling sub-clones of unstable parents. These predictions have been tested in this study primarily by tracking the karyotypic distribution of chromosomal rearrangements in clones and sub-clones exhibiting radiation-induced genomic instability; inheritance of mutator phenotypes was also analyzed. The results indicate that genomic instability is unevenly transmitted to sibling sub-clones, that chromosomal rearrangements within unstable clones are non-randomly distributed throughout the karyotype, and that the majority of chromosomal rearrangements associated with instability affect trisomic chromosomal segments. Observations of instability in trisomic regions suggests that in addition to promoting further alterations in chromosomal number, aneuploidy can affect the recovery of structural rearrangements. In summary, these findings cannot be fully explained by invoking a homogeneously distributed factor acting in trans, but do provide support for previous suggestions that genomic instability may in part be driven by a cis-acting mechanism.     

The complete mitochondrial genome of the Antarctic sea spider Ammothea carolinensis (Chelicerata; Pycnogonida)

Mitochondria are responsible for the oxidative phosphorylation process. Accordingly, putatively adaptive changes in their genomic features have been variously associated with major eco-physiological shifts in animal evolution, including increased metabolic rates and heat adaptation. Antarctic pycnogonids offer an interesting system to test whether the selective pressure for heat production and increased aerobic metabolism may be driving genomic changes like: (a) unusual compositional biases at the nucleotide and amino acid level, possibly related to cold adaptation; (b) an accelerated rate of mutations/genomic rearrangements, possibly related to the mutagenic effects of oxygen intermediates. The complete mitochondrial genome (mtDNA) of the Antarctic sea spider Ammothea carolinensis Leach, 1814 (Arthropoda: Pycnogonida), the type species for the genus Ammothea, has been determined and is here compared to known genomes from Antarctic and temperate species. We describe a marked heterogeneity in base composition skewness parameters as well as a strong signature of purifying selection toward an increase in thymines at second codon positions, possibly associated with an increased stability of hydrophobic inter-membrane domains. We further observe a fairly high rate of genomic changes, including a possible hot spot of recombination at the level of tRNA-Q. Nevertheless, these features do not seem to be restricted to the two Antarctic pycnogonids analyzed, as to suggest a causal relationship between cold adaptation and genomic changes, and are better interpreted as basal features shared by the entire group. The relevance of the newly determined sequence for the phylogeny of pycnogonids, including its base composition and genomic rearrangements, is further discussed.