Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species

LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.     

沙芥属(十字花科)的起源、分类与进化研究进展

沙芥属(PugioniumGaertn.)最初是从匙荠属(Bunias)中分出来单独建立的属,ndhF系统树表明,该属和高河菜属(Megacarpaea)、Farsetia、香雪球属(Lobularia)、屈曲花属(Iberis)和Ionopsidium亲缘关系较近,且和高河菜属构成姐妹关系。自从沙芥属确立以来,先后发表过沙芥[P.cornutum(L.)Gaertn]、斧形沙芥(P.dolabratum Maxim.)、距果沙芥(P.calcaratum Kom.)、鸡冠沙芥(P.cristatum Kom.)、翅果沙芥(P.pterocarpum Kom.)等5个种和宽翅沙芥(P.dolabratumvar.platypterum H.L.Yang)1个变种,但形态统计学和分子生物学的证据表明,沙芥属应该仅包含沙芥(P.cornutum)和斧形沙芥(P.dolabratum)2个形态学物种。基于不同遗传背景的DNA分子标记的研究结果进一步表明,沙芥和斧形沙芥这2个形态学物种间的遗传分化明显,但种间分化的时间并不久远,它们很可能是更新世以来随中亚和中国西北沙漠发展扩张而形成的2个近期分化的姐妹种。该文对沙芥属的系统起源、属下分类和遗传进化方面的研究历史和最新研究进展进行综述,并提出了研究中存在的问题。     

辣根属和豆瓣菜属(十字花科)系统位置的分子证据

对十字花科葶苈族的辣根属、南芥族的豆瓣菜属及相关属种植物的叶绿体DNA的trnL内含子和trnL-F基因间隔区序列进行了测定分析。结果表明,辣根属植物与南芥族的山芥属、蔊菜属、豆瓣菜属、碎米荠属在系统发育树中聚成一支,与葶苈族的模式属葶苈属植物相隔较远,结合形态特征,本研究认为辣根属应从葶苈族移出,其系统位置应靠近山芥属、蔊菜属、豆瓣菜属、碎米荠属植物;此外,系统发育树中,豆瓣菜属植物并入碎米荠属中,表明二者具有更近的亲缘关系,本研究结果不支持《中国植物志》第33卷对辣根属和豆瓣菜属的系统位置的处理。     

Evolution of genome size in Brassicaceae

BACKGROUND AND AIMS: Brassicaceae, with nearly 340 genera and more than 3350 species, anchors the low range of angiosperm genome sizes. The relatively narrow range of DNA content (0.16 pg < 1C < 1.95 pg) was maintained in spite of extensive chromosomal change. The aim of this study was to erect a cytological and molecular phylogenetic framework for a selected subset of the Brassicacae, and use this as a template to examine genome size evolution in Brassicaceae. METHODS: DNA contents were determined by flow cytometry and chromosomes were counted for 34 species of the family Brassicaceae and for ten Arabidopsis thaliana ecotypes. The amplified and sequenced ITS region for 23 taxa (plus six other taxa with known ITS sequences) were aligned and used to infer evolutionary relationship by parsimony analysis. KEY RESULTS: DNA content in the species studied ranged over 8-fold (1C = 0.16-1.31 pg), and 4.4-fold (1C = 0.16-0.71 pg) excluding allotetraploid Brassica species. The 1C DNA contents of ten Arabidopsis thaliana ecotypes showed little variation, ranging from 0.16 pg to 0.17 pg. CONCLUSIONS: The tree roots at an ancestral genome size of approximately 1x = 0.2 pg. Arabidopsis thaliana (1C = 0.16 pg; approximately 157 Mbp) has the smallest genome size in Brassicaceae studied here and apparently represents an evolutionary decrease in genome size. Two other branches that represent probable evolutionary decreases in genome size terminate in Lepidium virginicum and Brassica rapa. Branches in the phylogenetic tree that represent probable evolutionary increases in genome size terminate in Arabidopsis halleri, A. lyrata, Arabis hirsuta, Capsella rubella, Caulanthus heterophyllus, Crucihimalaya, Lepidium sativum, Sisymbrium and Thlaspi arvense. Branches within one clade containing Brassica were identified that represent two ancient ploidy events (2x to 4x and 4x to 6x) that were predicted from published comparative mapping studies.     

Comparative genome mapping reveals evidence of gene conversion between Sox9 paralogs of rainbow trout (Oncorhynchus mykiss)

Considerable evidence suggests that one genome duplication event preceded the divergence of teleost fishes and a second genome duplication event occurred before the radiation of teleosts of the family Salmonidae. Two Sox9 genes have been isolated from a number of teleosts and are called Sox9a and Sox9b. Two Sox9 gene copies have also been isolated from rainbow trout, a salmonid fish and are called Sox9 and Sox9α2. Previous evaluations of the evolutionary history of rainbow trout Sox9 gene copies using phylogenetic reconstructions of their coding regions indicated that they both belong to the Sox9b clade. In this study, we determine the true evolutionary history of Sox9 gene copies in rainbow trout. We show that the locus referred to as Sox9 in rainbow trout is itself duplicated. Mapping of the duplicated Sox9 gene copies indicates that they are co-orthologs of Sox9b while mapping of Sox9α2 indicates that it is an ortholog of Sox9a. This relationship is supported by phylogenetic reconstruction of Sox9 gene copies in teleosts using their 3′ untranslated regions. The conflicting phylogenetic topology of Sox9 genes in rainbow trout indicates the occurrence of gene conversion events between Sox9 and Sox9α2 which is supported by a number of recombination analyses.     

Intramolecular homologous recombination in Bacillus subtilis 168

Summary Ribosomal protein synthesis is regulated by controlling the fraction of mRNA associated with polysomes. It is known that this value changes in different developmental stages during Xenopus embryogenesis or, more generally, with changing cell growth conditions. We present here an analysis of the proportion of mRNA loaded on polysomes, carried out with probes for five different ribosomal proteins on several batches of Xenopus embryos obtained from different individuals. The results obtained indicate the existence of probe-dependent and individual differences, which reflect genetic variations in the cis- and trans-acting regulatory elements responsible for translational regulation. The fraction of ribosomal protein mRNA loaded onto polysomes can be used as an index of an individual's capacity for ribosome production.     

蕨类植物叶绿体基因ycf94的分子进化研究

ycf94基因是近年来在叶绿体基因组中新发现的一个基因,在蕨类植物中表现高度保守。该研究共选取94种蕨类植物,在系统发育背景下,对ycf94基因的结构特征、密码子偏好性、进化速率和适应性进化进行分析。结果表明, ycf94基因的密码子偏好性较弱,偏好使用以A/U结尾的密码子,且不同物种间的偏好性存在一定差异。密码子偏好性的形成主要受到突变压的影响,同时也存在其他因素的作用;基于凤尾蕨科和其他蕨类中ycf94基因的结构特征存在区别,对两者的分子替换速率进行了比较,表明颠换率、非同义替换率和ω值间存在显著差异;仅检测出1个正选择位点74A,强烈的负选择作用表明ycf94基因的结构和功能基本趋于稳定。这为蕨类系统发育分析提供了新依据,并提供了解析ycf94基因功能的线索。     

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

Background  

All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.     

Polymorphism of the S -locus glycoprotein gene ( SLG ) and the S -locus related gene ( SLR1 ) in Raphanus sativus L. and self-incompatible ornamental plants in the Brassicaceae

The S-locus glycoprotein gene, SLG, which participates in the pollen-stigma interaction of self-incompatibility, and its unlinked homologue, SLR1, were analyzed in Raphanus sativus and three self-incompatible ornamental plants in the Brassicaceae. Among twenty-nine inbred lines of R. sativus, eighteen S haplotypes were identified on the basis of DNA polymorphisms detected by genomic Southern analysis using Brassica SLG probes. DNA fragments of SLG alleles specifically amplified from eight S haplotypes by PCR with class I SLG-specific primers showed different profiles following polyacrylamide gel electrophoresis, after digestion with a restriction endonuclease. The nucleotide sequences of the DNA fragments of these eight R. sativus SLG alleles were determined. Degrees of similarity of the nucleotide sequences to a Brassica SLG (S  ⁶ SLG) ranged from 85.6% to 91.9%. Amino acid sequences deduced from these had the twelve conserved cysteine residues and the three hypervariable regions characteristic of Brassica SLGs. Phylogenetic analysis of the SLG sequences from Raphanus and Brassica revealed that the Raphanus SLGs did not form an independent cluster, but were dispersed in the tree, clustering together with Brassica SLGs. These results suggest that diversification of the SLG alleles of Raphanus and Brassica occurred before differentiation of these genera. Although SLR1 sequences from Orychophragmus violaceus were shown to be relatively closely related to Brassica and Raphanus SLR1 sequences, DNA fragments that are highly homologous to the Brassica SLG were not detected in this species. Two other ornamental plants in the Brassicaceae, which are related more distantly to Brassica than Orychophragmus, also lacked sequences highly homologous to Brassica SLG genes. The evolution of self-incompatibility in the Brassicaceae is discussed. Received: 9 October 1997 / Accepted: 27 January 1998     

Neutral Evolution of Synonymous Base Composition in the Brassicaceae

The GC content of synonymous sites is elevated in genes from both Brassica oleraceae and Arabidopsis lyrata compared with Arabidopsis thaliana. However, this shift in base composition is independent of gene expression level, and there is no evidence for a similar difference in the frequency of codons preferred by translational selection. The results suggest that composition evolution is caused by a change in mutation bias or biased gene conversion, rather than by a reduction in the efficacy of natural selection in selfing Arabidopsis. [Reviewing Editor: Dr. Magrus Nordborg]     

Genome Analysis inNeurospora crassa;Cloning of Four Lociarginine-1(arg-1),methionine-6(met-6),unknown-7(un-7), andribosome production-1(rip-1) and Associated Chromosome Walking

We have cloned fourNeurospora crassagenes by complementation analysis. Cloned genes include thearginine-1(arg-1),methionine-6(met-6),unknown-7(un-7), andribosome production-1(rip-1) loci. Chromosome walks were initiated in ordered cosmid libraries from the cloned loci. A total of about 700 kb of theNeurosporagenome is covered in these walks.     

Evolution of phenotypic integration in Brassica (Brassicaceae)

Phenotypic integration is a necessary characteristic of living organisms that results from genetic, developmental, and functional relationships among traits. The nature of these relationships can be influenced by the environment. We examined patterns of phenotypic integration of six species of rapid cycling Brassica and of Raphanus sativus within a phylogenetic context. Specifically, we tested the hypothesis that hybrid species show intermediate levels of integration in morphological and life-history characters compared to their putative parentals. We used matrix correlation tests to examine if cytogenetic relationships or ecological similarities among species partially explained the patterns of phenotypic integration. There was a significant negative relationship between the ecological and cytogenetic matrices, suggesting that more closely related species were ecologically dissimilar. However, neither ecological nor cytogenetic matrices significantly explained differences among species in the pattern of their phenotypic correlations. Set correlation analysis indicated that important traits within the modules and the strength of the correlations within modules differed across species. We also found that there were a greater number of significant correlations between modules than within modules. Hybrid species were more integrated (had greater number of significant trait correlations) than either of their parents, both within and between modules. However, univariate analyses of character means of the hybrid species were not significantly different from the combined mean of their putative parents for 5, 6, or 7 of the 11 phenotypic characters (for Brassica napus, B. juncea and B. carinata, respectively); for the remaining characters, the hybrids were more similar to one of the parents.     

宽翅菘蓝系统发育关系和分类地位研究

宽翅菘蓝(Isatis violascens)是分布于新疆准噶尔盆地的一种早春短命植物。基于形态的相似性,有人建议将宽翅菘蓝作为Isatis emarginata同义体。目前宽翅菘蓝尚未得到分子水平的研究,其系统发育地位也不清楚。该研究对宽翅菘蓝的ITS区进行测序,结合GenBank数据库中菘蓝属物种的ITS序列对宽翅菘蓝的系统关系和分类地位进行研究。最大简约法,最大似然法和贝叶斯法3种方法分析表明:菘蓝属物种聚为两个分支;宽翅菘蓝与I.emarginata和小果菘蓝具有较近的亲缘关系;基于形态相似性和较近的遗传距离,支持将宽翅菘蓝与I.emarginata合并为一个物种,并把宽翅菘蓝作为I.emarginata的同义种。     

Gene-directed mutagenesis on the chromosome of Bacillus subtilis 168

Summary We have devised a method whereby any mutagenized cloned DNA from Bacillus subtilis can be reinserted at the original site on the B. subtilis chromosome. The procedure depends on the accuracy and high frequency of homologous recombination between the B. subtilis chromosome and the DNA taken up by the cell. The method makes use of two drug resistance selection markers (the chloramphenicol resistance gene and the neomycin resistance gene) and a marker gene which functions as a catalyst. The utility of the method has been demonstrated using leuB and pro of B. subtilis as target gene and catalyst, respectively, and mutations such as leuB: : cat, leuB ^–, and pro: : neo constructed in vitro on the cloned DNA fragments. Transformation in sequential steps as (leuB ⁺ pro⁺)(leuB: : cat pro ⁺) (leuB ^– pro: : neo)(leuB ^– pro ⁺) resulted in a leuB ^– single mutant without affecting other regions of the B. subtilis chromosome (gene-directed mutagenesis). We also demonstrate that other single mutations such as metD ^– and pro ^–, as well as the double mutation leuB ^– pro ^– can be introduced by the same procedure. In principle, true isogenies with multiple mutations can be constructed by the method described in this paper. Furthermore, the procedure should be generally applicable to any organisms in which homologous recombination is proficient.     

Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages

Background

Gene duplication provides opportunities for lineage diversification and evolution of developmental novelties. Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization), or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization), or by the partitioning of original gene subfunctions between the duplicates (subfunctionalization). The Pax2/5/8 family of important developmental regulators has undergone parallel expansion among chordate groups. After the divergence of urochordate and vertebrate lineages, two rounds of independent gene duplications resulted in the Pax2, Pax5, and Pax8 genes of most vertebrates (the sister group of the urochordates), and an additional duplication provided the pax2a and pax2b duplicates in teleost fish. Separate from the vertebrate genome expansions, a duplication also created two Pax2/5/8 genes in the common ancestor of ascidian and larvacean urochordates.

Results

To better understand mechanisms underlying the evolution of duplicated genes, we investigated, in the larvacean urochordate Oikopleura dioica, the embryonic gene expression patterns of Pax2/5/8 paralogs. We compared the larvacean and ascidian expression patterns to infer modular subfunctions present in the single pre-duplication Pax2/5/8 gene of stem urochordates, and we compared vertebrate and urochordate expression to infer the suite of Pax2/5/8 gene subfunctions in the common ancestor of olfactores (vertebrates + urochordates). Expression pattern differences of larvacean and ascidian Pax2/5/8 orthologs in the endostyle, pharynx and hindgut suggest that some ancestral gene functions have been partitioned differently to the duplicates in the two urochordate lineages. Novel expression in the larvacean heart may have resulted from the neofunctionalization of a Pax2/5/8 gene in the urochordates. Expression of larvacean Pax2/5/8 in the endostyle, in sites of epithelial remodeling, and in sensory tissues evokes like functions of Pax2, Pax5 and Pax8 in vertebrate embryos, and may indicate ancient origins for these functions in the chordate common ancestor.

Conclusion

Comparative analysis of expression patterns of chordate Pax2/5/8 duplicates, rooted on the single-copy Pax2/5/8 gene of amphioxus, whose lineage diverged basally among chordates, provides new insights into the evolution and development of the heart, thyroid, pharynx, stomodeum and placodes in chordates; supports the controversial conclusion that the atrial siphon of ascidians and the otic placode in vertebrates are homologous; and backs the notion that Pax2/5/8 functioned in ancestral chordates to engineer epithelial fusions and perforations, including gill slit openings.     

Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae

Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.     

Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae

The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsy retrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.