Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora

The sporadic distribution of similar introns in organelle, nuclear ribosomal RNA and bacteriophage genes suggests that at least some of these introns are mobile genetic elements. Some plasmids in fungal mitochondria contain intron-like sequences and, like introns, they have scattered distributions within and among species. The occurrence and evolutionary importance of such horizontal transfer of DNA, not only between fungi, but among a wide range of organisms have been matters of much discussion. Here, we report experimental evidence for transfer of Neurospora mitochondrial plasmids from one mitochondrial genotype to another at high frequency during unstable vegetative cell fusion. Exchange of mitochondrial and nuclear genomes can also occur. These observations suggest that vegetative fusion may have a more important role in the mitochondrial genetic structure of natural populations than is generally thought, and may provide an explanation for the distribution of certain plasmids and possibly other mobile genetic elements.     

4种昆虫基因组中的线粒体假基因

为了进一步了解昆虫核基因组中线粒体假基因(Numts)序列分布情况,避免Numts序列对基于线粒体DNA(mtDNA)进行系统发育关系研究结果的误导,利用Blast N对GenBank中已完成核基因组和mtDNA测序的4种昆虫核基因组中的Numts序列进行检索,结果表明:冈比亚按蚊Anopheles gambiae中没有Numts序列;黑腹果蝇Drosophila melanogaster中仅有少量Numts序列;赤拟谷盗Tribolium castaneum和意大利蜜蜂Apis melliera基因组中Numts序列超过100条,尤其是意大利蜜蜂中的Numts序列涵盖全部mtDNA.ND2,ND4,ND5,COⅠ与lrRNA向核内转移频率高于其他mtDNA基因片段,因此,在使用其进行系统发育关系研究时需加倍谨慎.     

Nuclear DNA sequences detect species limits in ancient moa

Ancient DNA studies have typically used multi-copy mitochondrial DNA sequences. This is largely because single-locus nuclear genes have been difficult to recover from sub-fossil material, restricting the scope of ancient DNA research. Here, we have isolated single-locus nuclear DNA markers to assign the sex of 115 extinct moa and, in combination with a mitochondrial DNA phylogeny, tested competing hypotheses about the specific status of moa taxa. Moa were large ratite birds that showed extreme size variation both within and among species. For some taxa, this large variation was hypothesized to represent sexual dimorphism, while for others it was argued to reflect the existence of different species. Our results show that moa were characterized by extreme reverse sexual dimorphism and as a result we have been able to clarify the number of moa species. For example, we show that the three recognized 'species' of Dinornis comprised only two monophyletic groups and that two of these 'species' comprised individuals of one sex only. This study also illustrates that single-locus nuclear DNA sequences can be consistently recovered from ancient material.     

Molecular evidence regarding the origin of echolocation and flight in bats

Bats (order Chiroptera) are one of the few orders of mammals that echolocate and the only group with the capacity for powered flight. The order is subdivided into Microchiroptera and Megachiroptera, with an array of characteristics defining each group, including complex laryngeal echolocation systems in microbats and enhanced visual acuity in megabats. The respective monophylies of the two suborders have been tacitly assumed, although microbat monophyly is uncorroborated by molecular data. Here we present a phylogenetic analysis of bat relationships using DNA sequence data from four nuclear genes and three mitochondrial genes (total of 8,230 base pairs), indicating that microbat families in the superfamily Rhinolophoidea are more closely related to megabats than they are to other microbats. This implies that echolocation systems either evolved independently in rhinolophoids and other microbats or were lost in the evolution of megabats. Our data also reject flying lemur (order Dermoptera) as the bat sister group, indicating that presumed shared derived characters for flying lemurs and bats are convergent features that evolved in association with gliding and flight, respectively.     

Independent evolution of structural and coding regions in a Neurospora mitochondrial intron

The discovery of intervening sequences (introns) in eukaryotic genes has raised questions about the origin and evolution of these sequences. Hypotheses concerning these topics usually consider the intron as a unit that could be lost or gained over time, or as a region within which recombination can occur to facilitate the production of new proteins by exon shuffling. Additional complexities are observed in introns of mitochondrial and chloroplast genes which contain secondary structures required for messenger RNA splicing and open-reading frames encoding proteins. Here we describe differences in the organization of protein-coding sequences in the intron of the mitochondrial ND1 gene in two closely related species of Neurospora. These differences show that intron sequences involved in secondary structure formation and in protein coding can evolve as physically distinct elements. Indeed, the secondary structure elements of the ND1 intron can contain two different coding sequences located at two different positions within the intron.     

Widespread horizontal transfer of mitochondrial genes in flowering plants

Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.     

The origin of red algae and the evolution of chloroplasts

Chloroplast structure and genome analyses support the hypothesis that three groups of organisms originated from the primary photosynthetic endosymbiosis between a cyanobacterium and a eukaryotic host: green plants (green algae + land plants), red algae and glaucophytes (for example, Cyanophora). Although phylogenies based on several mitochondrial genes support a specific green plants/red algae relationship, the phylogenetic analysis of nucleus-encoded genes yields inconclusive, sometimes contradictory results. To address this problem, we have analysed an alternative nuclear marker, elongation factor 2, and included new red algae and protist sequences. Here we provide significant support for a sisterhood of green plants and red algae. This sisterhood is also significantly supported by a multi-gene analysis of a fusion of 13 nuclear markers (5,171 amino acids). In addition, the analysis of an alternative fusion of 6 nuclear markers (1,938 amino acids) indicates that glaucophytes may be the closest relatives to the green plants/red algae group. Thus, our study provides evidence from nuclear markers for a single primary endosymbiosis at the origin of these groups, and supports a kingdom Plantae comprising green plants, red algae and glaucophytes.     

Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis

The ratite moa (Aves; Dinornithiformes) were massive graviportal browsers weighing up to 250 kg (ref. 1) that dominated the New Zealand biota until their extinction approximately 500 yr ago. Despite an extensive Quaternary fossil record, moa taxonomy remains problematic and currently 11 species are recognized. Three Dinornis species were found throughout New Zealand and differed markedly in size (1-2 m height at back) and mass (from approximately 34 to 242 kg). Surprisingly, ancient mitochondrial DNA sequences show that the three species were genetically indistinguishable within each island, but formed separate North and South Island clades. Here we show, using the first sex-linked nuclear sequences from an extinct species, that on each island the three morphological forms actually represent just one species, whose size varied markedly according to sex and habitat. The largest females in this example of extreme reversed sexual size dimorphism were about 280% the weight and 150% the height of the largest males, which is unprecedented among birds and terrestrial mammals. The combination of molecular and palaeontological data highlights the difficulties of analysing extinct groups, even those with detailed fossil records.     

Phylogenetic relationship and morphological evolution in the subfamily Limenitidinae （Lepidoptera： Nymphalidae）

The mitochondrial cytochrome oxidase subunit I （CO1） gene and the nuclear elongation factor 1 α（EF-1α） gene were sequenced from 29 species of Nymphalidae （Nymphalidae, Lepidoptera）. Phylogenetic trees were constructed based on the sequences determined from the 29 species and sequences of other 36 species deposited in GenBank using the neighbor-joining （NJ）, maximum likelihood （ML） and Bayesian methods with Libythea celtis （Libytheinae） as the outgroup. Our phylogenetic trees indicated four major clades. Clade A includes three subfamilies： Apaturinae, Nymphalinae, and Limenitidinae, excluding the tribe Limenitidini; Clade B includes the subfamilies Heliconiinae and the tribe Limenitidini; Clade C includes Satyrinae, Calinaginae, Charaxinae and Morphinae; and Clade D includes subfamily Danainae. Our study suggested that the tribes Pseudergolini, Biblidini, Limenitidini and Cyrestidini should be considered as subfamilies and confirmed the interspecific relationships within the subfamily Pseudergolinae, namely Amnosia ＋（Pseudergolis ＋ （Stibochiona ＋ Dichorragia））. We then mapped three morphological characters （spot of anal angle, eyespots, and process from outer margin of hind wing） onto the phylogenetic tree constructed by ML analysis using the combined sequence data. Based on this the evolutionary patterns of these morphological characters were identified, they indicated that the three characters evolved repeatedly in the family Nymphalidae.     

广西5种常见星虫动物的线粒体基因组特征和系统进化分析

为探明广西北部湾星虫动物的线粒体基因组遗传变异和基因序列特征,采用高通量测序测定广西北部湾5种常见星虫动物的线粒体基因组,并对其基因序列特征、遗传变异、系统进化进行分析。结果显示,星虫动物线粒体基因组具有典型的无脊椎动物线粒体基因组的特征,基因排列高度保守,特别是其13个蛋白质编码基因（PCGs）。此外,星虫动物线粒体基因组的基因均编码在H链上,并存在3个高度保守的基因排列区块,与环节动物和螠虫动物线粒体基因组特征较为相似。cox1、cox2和cob等3个基因进化速率最慢、遗传变异水平最低,适合作为星虫动物种属系统进化研究以及不同种间生物条形码构建的分子标记。nad6、nad4、nad5和nad2等4个基因的遗传变异水平较高（大于60%）,变异位点数量较多,适合作为星虫动物种群遗传多样性研究的分子标记。星虫动物线粒体13个蛋白质编码基因的Ka/Ks比值均低于1（0.058 2-0.726 6）,其中cox1、cox3和cob等3个基因的Ka/Ks比值最低（小于0.1）,表明在星虫动物线粒体遗传进化过程中,这3个蛋白质编码基因承受强烈的自然选择压力和功能束缚。基于线粒体基因组蛋白质编码基因系统进化树的研究结果表明,星虫动物可分为方格星虫纲和革囊星虫纲两个进化分支,星虫动物与环节动物的进化地位、亲缘关系较近,而与软体动物的亲缘关系较远。本研究结果不仅为广西北部湾特色星虫动物渔业资源多样性调查和保护提供分子遗传数据,也为星虫动物系统进化研究提供了科学参考。     

即刻早基因ZENK的基因功能及其应用进展

即刻早基因ZENK是核基因组内编码转录因子的单拷贝基因,它受多种胞外信号,如血清、生长因子、细胞因子和激素的作用在不同类型细胞内迅速、大量表达.ZENK蛋白通过C2H2型锌指识别靶基因启动子中的GC丰富序列并发生作用,从而调控靶基因的转录.ZENK基因参与细胞生长、分化、发育的调控,而且其在大脑的诱导表达与动物的学习、记忆密切关联.另有研究显示,ZENK具有很高的进化保守性,可以作为新的分子标记运用于分子系统学研究.     

Mitochondrial DNA repairs double-strand breaks in yeast chromosomes

The endosymbiotic theory for the origin of eukaryotic cells proposes that genetic information can be transferred from mitochondria to the nucleus of a cell, and genes that are probably of mitochondrial origin have been found in nuclear chromosomes. Occasionally, short or rearranged sequences homologous to mitochondrial DNA are seen in the chromosomes of different organisms including yeast, plants and humans. Here we report a mechanism by which fragments of mitochondrial DNA, in single or tandem array, are transferred to yeast chromosomes under natural conditions during the repair of double-strand breaks in haploid mitotic cells. These repair insertions originate from noncontiguous regions of the mitochondrial genome. Our analysis of the Saccharomyces cerevisiae mitochondrial genome indicates that the yeast nuclear genome does indeed contain several short sequences of mitochondrial origin which are similar in size and composition to those that repair double-strand breaks. These sequences are located predominantly in non-coding regions of the chromosomes, frequently in the vicinity of retrotransposon long terminal repeats, and appear as recent integration events. Thus, colonization of the yeast genome by mitochondrial DNA is an ongoing process.     

水稻配子体细胞质雄性不育基因orf79/orfH79的变异多态性研究

线粒体基因组异常嵌合基因orf79/orfH79被证实为水稻配子体细胞质雄性不育（cytoplasmic male sterility,CMS）基因。为了调查配子体CMS基因orf79/orfH79在水稻资源中的遗传与变异,来自不同国家的31份水稻材料被用于PCR检测。10份水稻材料被检测出具有配子体CMS基因orf79/orfH79,表明配子体CMS基因orf79/orfH79在水稻资源中具有较高的分布频率（32.2%）。DNA序列分析显示水稻配子体CMS基因orf79/orfH79具有非常保守的遗传特性（98.3%）,只有4个多态性碱基位点被检测出,4个碱基位点的变异导致多肽ORF79/ORFH79三个氨基酸位点的改变。基于orf79/orfH79 DNA序列的聚类分析系显示10份水稻材料被分成了3个类群,表明配子体CMS胞质在水稻资源中存在多种变异模式。研究结果为新水稻CMS胞质的发掘与培育提供重要的理论和实验依据。     

Molecular phylogenetic evidence that the Chinese viviparid genus Margarya (Gastropoda: Viviparidae) is polyphyletic

We investigated the phylogeny of the viviparid genus Margarya,endemic to Yunnan,China,using two mitochondrial gene fragments(COI and 16S rRNA).The molecular phylogeny based on the combined dataset indicates that Margarya is polyphyletic,as two of the three well-supported clades containing species of Margarya also comprise species from other viviparid genera.In one clade,sequences of four species of Margarya even cluster indiscriminately with those of two species of Cipangopaludina,indicating that the current state of Asian viviparid taxonomy needs to be revised.Additionally,these data suggest that shell evolution in viviparids is complex,as even the large and strongly sculptured shells of Margarya,which are outstanding among Asian viviparids,can apparently be easily converted to simple smooth shells.The molecular data also indicate that the species status of the six extant species of Margarya should be re-assessed.     

Sequencing and analysis of the complete mitochondrial DNA of Russell's snapper (L.russellii)

The entire mitochondrial DNA sequence (mitogenome) of Russell's snapper (Lutjanus russellii) was determined using long PCR and primer-walking methodology,representing the first complete mitogenome accessioned for Lutjanid fishes (16,505 bp,GenBank Accession No.EF514208).The mitogenome was similar in gene composition and order to those of other vertebrates,having 37 structural genes,i.e.,two ribosomal RNAs,22 transfer RNAs,and 13 protein-coding genes.Phylogenetic analyses based on the mtDNA sequence of Russell's snapper supported a close relationship between Lutjaninae and Caesioninae,consistent with taxonomic hypotheses based on morphology.More studies utilizing mitogenomes are needed to resolve high-level relationships among snappers.     

Single gene circles in dinoflagellate chloroplast genomes.

Photosynthetic dinoflagellates are important aquatic primary producers and notorious causes of toxic 'red tides'. Typical dinoflagellate chloroplasts differ from all other plastids in having a combination of three envelope membranes and peridinin-chlorophyll a/c light-harvesting pigments. Despite evidence of a dinoflagellete satellite DNA containing chloroplast genes, previous attempts to obtain chloroplast gene sequences have been uniformly unsuccessful. Here we show that the dinoflagellate chloroplast DNA genome structure is unique. Complete sequences of chloroplast ribosomal RNA genes and seven chloroplast protein genes from the dinoflagellate Heterocapsa triquetra reveal that each is located alone on a separate minicircular chromosome: 'one gene-one circle'. The genes are the most divergent known from chloroplast genomes. Each circle has an unusual tripartite non-coding region (putative replicon origin), which is highly conserved among the nine circles through extensive gene conversion, but is very divergent between species. Several other dinoflagellate species have minicircular chloroplast genes, indicating that this type of genomic organization may have evolved in ancestral peridinean dinoflagellates. Phylogenetic analysis indicates that dinoflagellate chloroplasts are related to chromistan and red algal chloroplasts and supports their origin by secondary symbiogenesis.     

Origin and evolution of new exons in the rodent zinc finger protein 39 gene

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.     

DNA transformation leads to pilin antigenic variation in Neisseria gonorrhoeae

Many pathogenic bacteria express pili (fimbriae) on their cell surfaces. These structures mediate binding of bacteria to host tissues, and may also be involved in other aspects of pathogenesis. Neisseria gonorrhoeae pili are mainly composed of a single protein, pilin, whose expression is controlled at chromosomal expression loci (pilE). An intact pilin gene and promoter sequences are only found at pilE. Strain MS11 contains two expression sites (pilE1 and pilE2), whereas several of its derivatives and other clinical isolates contain only one. Silent pilin loci (pilS1-pilS7) contain truncated variant pilin genes lacking the promoter and conserved pilin gene sequences. Pilin antigenic variation in N. gonorrhoeae occurs by DNA recombination between one of he silent partial variant gene segments in pilS and an expressed pilin gene in pilE. The recombination reactions are nonreciprocal, and therefore the mechanism has been classified as gene conversion. We report that much of the recombination between pilin loci actually occurs after transformation of living piliated cells by DNA liberated from lysed cells within a population. This constitutes a new molecular mechanism for an antigenic variation system, as well as the first specific function for a DNA transformation system.     

Maternal inheritance in polyploid fish inferred from mitochondrial ATPase genes analysis

The sequences of the ATPase8/6 genes for the triploid, tetraploid and pentaploid hybrids as well as for their male parent blunt snout bream were determined. In order to examine mitochondrial maternal inheritance, the sequences were subjected to a comparative sequence analysis with the homologous sequences of red crucian carp, their female parent, and zebrafish as the outgroup. Base composition and variation as well as the divergences based on nucleotide sequences and deduced amino acid sequences were calculated. Phylogenetic trees were also constructed with maximum parsimony (MP), minimum evolution (ME), neighbor joining (NJ) and the unweighted pair group method with arithmetic mean (UPGMA) algorithms in MEGA 3.1. The results showed that most nucleotide substitutions occurred at the third codon position of the two genes and thus represented synonymous mutations. The nucleotide sequence divergences of the ATPase8/6 genes ranged from 0.0% to 21.6% among ingroup samples (three types of polyploids and their parents), and 27.0–28.2% between their ingroup and the outgroup samples. All the polyploids were considerably closer in sequence relationship to the female parent red crucian carp (0.0–3.3%) compared to their male parent blunt snout bream (21.0–21.6%). The phylogenetic trees also showed a similar result. In conclusion, the mitochondrial ATPase8/6 genes of artificial polyploid fish stringently indicated maternal inheritance. Our results also suggested that the ATPase8/6 genes are valuable genetic markers to track genealogies and variations in the progenies of the hybrids.