Segmented genome: elementary units of genome structure

Numerous observations, measurements and calculations strongly indicate that both eukaryotic and prokaryotic genomes are built as linear arrays of units of rather uniform size, about 400 base pairs. The units are likely to correspond to early individual genes that existed, presumably, in form of DNA circles. Their combinatorial fusion resulted eventually in formation of the early segmented genomes. The segmented structure of the genomes is, apparently, still maintained by some structural selection pressures. Some of the units can be recognized in the sequences by characteristic sequence motifs at the borders of the units. Identification and characterization of the units, their mapping on the genomes should become an important prerequisite of genome comparisons and genome evolution studies.     

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.     

Genome Size and Species Diversification

Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone.     

Genome compaction and stability in microsporidian intracellular parasites

Microsporidian genomes are extraordinary among eukaryotes for their extreme reduction: although they are similar in form to other eukaryotic genomes, they are typically smaller than many prokaryotic genomes. At the same time, their rates of sequence evolution are among the highest for eukaryotic organisms. To explore the effects of compaction on nuclear genome evolution, we sequenced 685,000 bp of the Antonospora locustae genome (formerly Nosema locustae) and compared its organization with the recently completed genome of the human parasite Encephalitozoon cuniculi. Despite being very distantly related, the genomes of these two microsporidian species have retained an unexpected degree of synteny: 13% of genes are in the same context, and 30% of the genes were separated by a small number of short rearrangements. Microsporidian genomes are, therefore, paradoxically composed of rapidly evolving sequences harbored within a slowly evolving genome, although these two processes are sometimes considered to be coupled. Microsporidian genomes show that eukaryotic genomes (like genes) do not evolve in a clock-like fashion, and genome stability may result from compaction in addition to a lack of recombination, as has been traditionally thought to occur in bacterial and organelle genomes.     

The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.     

Viral genome segmentation can result from a trade-off between genetic content and particle stability

The evolutionary benefit of viral genome segmentation is a classical, yet unsolved question in evolutionary biology and RNA genetics. Theoretical studies anticipated that replication of shorter RNA segments could provide a replicative advantage over standard size genomes. However, this question has remained elusive to experimentalists because of the lack of a proper viral model system. Here we present a study with a stable segmented bipartite RNA virus and its ancestor non-segmented counterpart, in an identical genomic nucleotide sequence context. Results of RNA replication, protein expression, competition experiments, and inactivation of infectious particles point to a non-replicative trait, the particle stability, as the main driver of fitness gain of segmented genomes. Accordingly, measurements of the volume occupation of the genome inside viral capsids indicate that packaging shorter genomes involves a relaxation of the packaging density that is energetically favourable. The empirical observations are used to design a computational model that predicts the existence of a critical multiplicity of infection for domination of segmented over standard types. Our experiments suggest that viral segmented genomes may have arisen as a molecular solution for the trade-off between genome length and particle stability. Genome segmentation allows maximizing the genetic content without the detrimental effect in stability derived from incresing genome length.     

Genome DNA content and chromosome organization in Gossypium

The ascending genome size in Gossypium is assumed to be D, A, B, E and F, and C. Feulgen cytophotometry revealed that mean value of DNA content for each genome was D= 10.95, B = 13.88, F = 14.31, E = 18.24, A = 18.66, and C = 20.30, and that there is a close relationship of genomic chromosome size and DNA content. Evidence suggests that the five genomes with large chromosomes arose from a D genome-like progenetor by large scale, saltatory replication of repetitive DNA distributed uniformly through the ancestral genome. Corresponding adjustment in recombination units did not accompany the two-fold divergence in DNA value of the two homoeologous A and D genomes in the allotetraploid species.     

The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

The small size of RNA virus genomes (2-to-32 kb) has been attributed to high mutation rates during replication, which is thought to lack proof-reading. This paradigm is being revisited owing to the discovery of a 3′-to-5′ exoribonuclease (ExoN) in nidoviruses, a monophyletic group of positive-stranded RNA viruses with a conserved genome architecture. ExoN, a homolog of canonical DNA proof-reading enzymes, is exclusively encoded by nidoviruses with genomes larger than 20 kb. All other known non-segmented RNA viruses have smaller genomes. Here we use evolutionary analyses to show that the two- to three-fold expansion of the nidovirus genome was accompanied by a large number of replacements in conserved proteins at a scale comparable to that in the Tree of Life. To unravel common evolutionary patterns in such genetically diverse viruses, we established the relation between genomic regions in nidoviruses in a sequence alignment-free manner. We exploited the conservation of the genome architecture to partition each genome into five non-overlapping regions: 5′ untranslated region (UTR), open reading frame (ORF) 1a, ORF1b, 3′ORFs (encompassing the 3′-proximal ORFs), and 3′ UTR. Each region was analyzed for its contribution to genome size change under different models. The non-linear model statistically outperformed the linear one and captured >92% of data variation. Accordingly, nidovirus genomes were concluded to have reached different points on an expansion trajectory dominated by consecutive increases of ORF1b, ORF1a, and 3′ORFs. Our findings indicate a unidirectional hierarchical relation between these genome regions, which are distinguished by their expression mechanism. In contrast, these regions cooperate bi-directionally on a functional level in the virus life cycle, in which they predominantly control genome replication, genome expression, and virus dissemination, respectively. Collectively, our findings suggest that genome architecture and the associated region-specific division of labor leave a footprint on genome expansion and may limit RNA genome size.     

Genome diversity in microbial eukaryotes

The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.     

Genome plasticity in Lactococcus lactis

Comparative genome analyses contribute significantly to our understanding of bacterial evolution and indicate that bacterial genomes are constantly evolving structures. The gene content and organisation of chromosomes of lactic acid bacteria probably result from a strong evolutionary pressure toward optimal growth of these microorganisms in milk. The genome plasticity of Lactococcus lactis was evaluated at inter- and intrasubspecies levels by different experimental approaches. Comparative genomics showed that the lactococcal genomes are not highly plastic although large rearrangements (a.o. deletions, inversions) can occur. Experimental genome shuffling using a new genetic strategy based on the Cre-loxP recombination system revealed that two domains are under strong constraints acting to maintain the original chromosome organisation: a large region around the replication origin, and a smaller one around the putative terminus of replication. Future knowledge of the rules leading to an optimal genome organisation could facilitate the definition of new strategies for industrial strain improvement.     

Genome Analysis of Three Species of the Genus Algropyron

The karyotype, C-banding, N-banding and meiosis of F1 plants and isoenzyme electrophoresis were analysed for the study of three species in Agropyron. It was showed that the B genome homologous to common wheat is not likely to exist in A. intermedium and the other two genomes were turned out to be homoeologous. The genome formula xE1 E2 was suggested for A. intermedium. The B genome was found not likely to exist in A. elongata (10x) either, there are two pairs of homoeologous genomes in this species and the genome formula xE1E2F1F2 was suggested. It seemed that the two genomes of A. elongata (4x) are not homoeologous.     

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.     

真菌基因组de novo测序组装的方法与实践

真菌基因组较其他真核生物基因组结构简单,长度短,易于测序、组装与注释,因此真菌基因组是研究真核生物基因组的模型。为研究真菌基因组组装策略,本研究基于Illumina HiSeq测序平台对烟曲霉菌株An16007基因组测序,分别使用5种de novo组装软件ABySS、SOAP-denovo、Velvet、MaSuRCA和IDBA-UD组装基因组,然后通过Augustus软件进行基因预测,BUSCO软件评估组装结果。研究发现,5种组装软件对基因组组装结果不同,ABySS组装的基因组较其他4种组装软件具有更高的完整性和准确性,且预测的基因数量较高,因此,ABySS更适合本研究基因组的组装。本研究提供了真菌de novo测序、组装及组装质量评估的技术流程,为基因组<100 Mb的真菌或其他生物基因组的研究提供参考。     

The Random Nature of Genome Architecture: Predicting Open Reading Frame Distributions

Background

A better understanding of the size and abundance of open reading frames (ORFS) in whole genomes may shed light on the factors that control genome complexity. Here we examine the statistical distributions of open reading frames (i.e. distribution of start and stop codons) in the fully sequenced genomes of 297 prokaryotes, and 14 eukaryotes.

Methodology/Principal Findings

By fitting mixture models to data from whole genome sequences we show that the size-frequency distributions for ORFS are strikingly similar across prokaryotic and eukaryotic genomes. Moreover, we show that i) a large fraction (60–80%) of ORF size-frequency distributions can be predicted a priori with a stochastic assembly model based on GC content, and that (ii) size-frequency distributions of the remaining “non-random” ORFs are well-fitted by log-normal or gamma distributions, and similar to the size distributions of annotated proteins.

Conclusions/Significance

Our findings suggest stochastic processes have played a primary role in the evolution of genome complexity, and that common processes govern the conservation and loss of functional genomics units in both prokaryotes and eukaryotes.     

Genome analysis of Theileria parva

Recent technological developments in the field of genome analyses have advanced our knowledge of the structures of prokaryotic and eukoryotic genomes. Examples of these range from small bacterial genomes, such as Escherichia coli, to the more complex genomes of Caenorhabditis elegans, Drosophila, humans and mouse. Here, Subhash Morzona and John Young review developments in mapping the genome of on economically important protozoan parasite o f cattle, Theileria parva. This map provides a framework for more detailed analysis of the genome structure o f this organism. The methodologies developed in constructing the map also have application to the mapping of other protozoan genomes.     

藻类植物叶绿体基因组研究进展

藻类植物的cpDNA结构复杂,普遍缺失反向重复序列IR,且存在IR的藻类植物种类的cpDNA也有IR变短退化迹象.藻类植物的cpDNA包含的基因一般比高等植物要多,编码能力更强.藻类植物cpDNA全序列的测定方法主要是Fosmid文库构建,配合使用Long-PCR技术.该文对国内外有关藻类植物叶绿体基因组结构、叶绿体编码基因、叶绿体基因组在藻类系统发育中的应用以及藻类植物叶绿体基因组的提取和序列测定方法等进行综述,为藻类植物的系统发育和叶绿体起源以及功能基因组学的研究提供理论依据.     

Genome sequence analyses of Pseudomonas savastanoi pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads

Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a common disease of soybean. In an effort to compare a current field isolate with one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076, were sequenced using 454 pyrosequencing. The genomes of both Psg strains share more than 4,900 highly conserved genes, indicating very low genetic diversity between Psg genomes. Though conserved, genome rearrangements and recombination events occur commonly within the two Psg genomes. When compared to each other, 437 and 163 specific genes were identified in B076 and race 4, respectively. Most specific genes are plasmid-borne, indicating that acquisition and maintenance of plasmids may represent a major mechanism to change the genetic composition of the genome and even acquire new virulence factors. Type three secretion gene clusters of Psg strains are near identical with that of P. savastanoi pv. phaseolicola (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the coronatine biosynthetic cluster is present on a large plasmid in strain B076, but not in race 4. In silico subtractive hybridization-based comparative genomic analyses with nine sequenced phytopathogenic pseudomonads identified dozens of specific islands (SIs), and revealed that the genomes of Psg strains are more similar to those belonging to the same genomospecies such as Pph 1448A than to other phytopathogenic pseudomonads. The number of highly conserved genes (core genome) among them decreased dramatically when more genomes were included in the subtraction, suggesting the diversification of pseudomonads, and further indicating the genome heterogeneity among pseudomonads. However, the number of specific genes did not change significantly, suggesting these genes are indeed specific in Psg genomes. These results reinforce the idea of a species complex of P. syringae and support the reclassification of P. syringae into different species.     

中间偃麦草染色体组构成的同工酶研究

应用聚丙烯酰胺凝胶电泳,研究了带有不同染色体组的各种小麦和中间偃麦草的酯酶、苹果酸脱氢酶、酸性或碱性磷酸酶同工酶的酶谱。通过对各酶谱与染色体组的对比分析表明,中间偃麦草不含与小麦B组或D组同源的染色体,而可能含有两组分别与小麦A组和提莫菲维小麦G组有些同源性的染色体。中间偃麦草的染色体组构成可用E_(A1)E_(A2)N_G或E_(G1)E_(G2)N_A表示。