The allopolyploid origin of kiwifruit,Actinidia deliciosa (Actinidiaceae)

The genetic origin of kiwifruit (Actinidia deliciosa var.deliciosa) was studied using phylogenetic analysis of DNA sequences derived from the polygalacturonase gene. Results indicate that hexaploid kiwifruit had an allopolyploid origin with the diploidA. chinensis contributing one genome (genome A) and another (as yet unidentified) diploid species contributing a second genome (genome B). The results leave open the question of whether a third, distinct species contributed to the hexaploid kiwifruit genome. A tetraploid race ofA. chinensis is also suggested to be allopolyploid containing genomes A and B.     

Relationships betweenOryza species (Poaceae) based on 5S DNA sequences

Relationships between 9Oryza species, covering 6 different genomes, have been studied using hybridization and nucleotide sequence information from the5S Dna locus. Four to five units of the major size class of 5S DNA in each species, 55 units in all, were cloned and sequenced. Both hybridization and sequence data confirmed the basic differences between the A and B, C, D genome species suggested by morphological and cytological data. The 5S DNA units of the A genome species were very similar, as were the ones from the B, C, and D genome-containing species. The 5S DNA ofO. australiensis (E genome) grouped with the B, C, D cluster, while the units ofO. brachyantha (F genome) were quite different and grouped away from all other species. 5S DNA units fromO. minuta, O. latifolia, O. australiensis, andO. brachyantha hybridized strongly, and preferentially, to the genomic DNA from which the units were isolated and hence could be useful as species/genome specific probes. The 5S DNA units fromO. sativa, O. nivara, andO. rufipogon provided A genome-specific probes as they hybridized preferentially to A genome DNA. The units fromO. punctata andO. officinalis displayed weaker preferential hybridization toO. punctata DNA, possibly reflecting their shared genome (C genome).     

药用植物华重楼(黑药花科)叶绿体全基因组研究

为探究华重楼(Paris polyphylla var. chinensis)的叶绿体基因组特征,利用叶绿体系统发育基因组学方法,对华重楼与其它百合目植物的叶绿体全基因组进行了比较。结果表明,华重楼的叶绿体全基因组长158307 bp,由4个区组成,包括2个反向重复区(IRA和IRB,27473 bp)、1个小单拷贝区(SSC,18175 bp)和1个大单拷贝区(LSC,85187 bp)。其叶绿体基因组有115个基因,包括81个编码蛋白质基因、30个转运RNA基因和4 个核糖体RNA基因。11种百合目植物的叶绿体全基因组的基因组成和基因顺序相似。华重楼的cemA基因是假基因,其起始密码子后有多聚核苷酸poly(A)及CA双核苷酸重复序列,编码序列中出现多个终止密码子, 且与北重楼(Paris verticillata)的cemA编码序列中的终止密码子位置不同。因此,华重楼叶绿体基因组比较保守;cemA结构及假基因化现象可能具有重要的进化与系统发育信息,其编码序列中的终止密码子可以区分华重楼和北重楼。     

Hybridisation,genomic constitution and generic delimitation inElymus s. l. (Poaceae: Triticeae)

Intergeneric crosses were made between representatives of the genomically-defined generaElymus, Agropyron, Elytrigia, Pseudoroegneria, andThinopyrum. The genomic constitution ofElytrigia repens, the type species ofElytrigia, is shown to be SSH, a genomic combination otherwise found only inElymus. The S genome ofPseudoroegneria has almost always a dominant influence on the morphology of the taxa of which it is a component.Wang (1989) showed that the J genome inThinopyrum and the S genome have considerable homoeology, with a mean c-value of 0.35 in diploid SJ hybrids. A genetic coherence from S to SJ^e, J^e, J^eJ^b, and J^b can be expected, agreeing with the continuous morphologic variation pattern observed. Because of the absence of morphological discontinuities between the taxa,Pseudoroegneria (S),Elymus (SH, SY, sometimes with additional genomes),Elytrigia (SSH, SSHX), andThinopyrum (SJ, SJJ, J) are best treated as a single genus,Elymus, following the generic concept ofMelderis in Flora Europaea and Flora of Turkey. The basic genomic constituents ofElymus will then be the S and/or J genomes.Agropyron, with diploids, tetraploids, and hexaploids based on the P genome is morphologically distinct from other genera inTriticeae. In a few species ofElymus andPseudoroegneria, a P genome is an additional constituent. In these cases the P genome has a negligible morphological influence. Therefore, it seems reasonable to maintainAgropyron as a separate genus.     

Origin and phylogeny of Oryza species with the CD genome based on multiple-gene sequence data

The CD genome species in the genus Oryza are endemic to Latin America, including O. alta, O. grandiglumis and O. latifolia. Origins and phylogenetic relationship of these species have long been in dispute and are still ambiguous due to their homogeneous genome type, similar morphological characteristics and overlapping distribution. In the present study, we sequenced two chloroplast fragments (matK and trnL-trnF) and portions of three nuclear genes (Adh1, Adh2 and GPA1) from sixteen accessions representing seven species with the C, CD, and E genomes, as well as one G genome species as the outgroup. Phylogenetic analyses using parsimony and distance methods strongly supported that the CD genome originated from a single hybridization event, and that the C genome species (O. officinalis or O. rhizomatis instead of O. eichingeri) served as the maternal parent while the E genome species (O. australiensis) was the paternal donor during the formation of CD genome. In addition, the consistent phylogenetic relationships among the CCDD species indicated that significant divergence existed between O. latifolia and the other two (O. alta and O. grandiglumis), which corroborated the suggestion of treating the latter two as a single species or as taxa within species.We thank Tao Sang of Michigan State University (East Lansing, USA) and Bao-rong Lu of Fudan University (Shanghai, China) for their encouragement and assistance. We are also grateful to the International Rice Research Institute (Manila, Philippines) for providing plant material for this study. This research was supported by the Chinese Academy of Sciences (kscxz-sw-101A), the National Natural Science Foundation of China (30025005) and the Program for Key International S & T Cooperation Project of P. R. China (2001CB711103).     

Phylogenetic analysis of questionable tetraploid species in Roegneria and Pseudoroegneria (Poaceae: Triticeae) inferred from a gene encoding plastid acety1-CoA carboxylase

To evaluate the phylogenetic relationships of questionable tetraploid species Roegneria alashanica Keng, Roegneria magnicaespes (D.F. Cui) L.B. Cai, Roegneria elytrigioides C. Yen et J.L. Yang, Roegneria grandis Keng and Pseudoroegneria geniculata (Trin.) Á. Löve, the single copy sequences of the plastid acetyl-CoA carboxylase gene (Acc1) were analyzed among the five species and the related diploid and tetraploid species. The results indicated that: (a) R. alashanica contained one set of modified St genome which was closely related to the E^e genome, and the other set of genome was closely related to the P genome; (b) R. magnicaespes contained one set of St genome, the other set of genome might be closely related to the P genome. There are close affinities between R. magnicaespes and R. alashanica; (c) R. elytrigioides contained two sets of St genomes, and it is reasonable to be treated as Pseudoreogneria elytrigioides (C. Yen et J.L. Yang) B.R. Lu; (d) the genome of R. grandis should be designed as St^gY. The St^g genome was a differentiated form of the St genome in Pseudoroegneria and was homoeologous with the Y genome in Roegneria; (e) the genomic constitution of P. geniculata was similar to that of R. magnicaespes and R. alashanica and distinctly related to P. geniculata ssp. scythica (E^eSt). They should be treated as different species in different genera; and (f) the Y genome was possibly originated from the St genome, and was sister to the St, E^e, E^b and W genomes.     

Evolutionary pattern of the gtwin retrotransposon in the Drosophila melanogaster subgroup

The gtwin retrotransposon was recently discovered in the Drosophila melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work.     

崖壁植物太行菊与长裂太行菊全基因组大小及特征分析北大核心CSCD

太行菊(Opisthopappus taihangensis)、长裂太行菊(O.longilobus),为太行山特有多年生崖壁草本植物,菊科(Compositae)重要野生资源,具有较高的经济与生态价值。为确定适合两物种的全基因组测序策略,该研究利用流式细胞法和高通量测序技术,分析两物种基因组大小、杂合率、重复序列及GC含量等信息。结果表明:(1)流式细胞法估算太行菊基因组大小约为2.1 Gb,长裂太行菊基因组大小约为2.4 Gb。(2)高通量测序修正后太行菊基因组大小为3.13 Gb,重复序列比例为84.35%,杂合度为0.99%,GC含量为36.56%;长裂太行菊基因组为3.18 Gb,重复序列比例为83.83%,杂合度为1.17%,GC含量为36.62%。(3)初步组装后GC含量分布及平均深度存在异常,出现分层现象,可能是两物种基因组杂合率较高所致。综上结果表明,太行菊、长裂太行菊均属于高重复、高杂合、大基因组的复杂基因组,建议使用Illumina+PacBio测序组装策略,进行全基因组测序分析。     

Genome analysis of species in the genus Hystrix (Triticeae; Poaceae)

Genomic in situ hybridisation (GISH) and Southern genomic hybridisation were applied in order to gain further knowledge regarding generic delimitation of the genus Hystrix as well as to clarify the genomes of the Hystrix species H. patula, H. longearistata, H. coreana, H. duthiei and H. komarovii. The hybridisation intensity of different genomic probes was compared among the Hystrix species and with other Triticeae species. The Southern- and GISH results confirm that H. patula contains the StH genome and show that H. komarovii most likely has a variant of this StH genome. The other Hystrix species under study, i.e. H. longearistata, H. coreana and H. duthiei, contain an Ns basic genome, and most probably two variants of this basic genome, Ns ¹ Ns ² . The genus Hystrix is thus not a monophyletic group of species.     

First Sequenced Mitochondrial Genome from the Phylum Acanthocephala(Leptorhynchoides thecatus) and Its Phylogenetic Position Within Metazoa

The complete sequence of the mitochondrial genome of Leptorhynchoides thecatus (Acanthocephala) was determined, and a phylogenetic analysis was carried out to determine its placement within Metazoa. The genome is circular, 13,888 bp, and contains at least 36 of the 37 genes typically found in animal mitochondrial genomes. The genes for the large and small ribosomal RNA subunits are shorter than those of most metazoans, and the structures of most of the tRNA genes are atypical. There are two significant noncoding regions (377 and 294 bp), which are the best candidates for a control region; however, these regions do not appear similar to any of the control regions of other animals studied to date. The amino acid and nucleotide sequences of the protein coding genes of L. thecatus and 25 other metazoan taxa were used in both maximum likelihood and maximum parsimony phylogenetic analyses. Results indicate that among taxa with available mitochondrial genome sequences, Platyhelminthes is the closest relative to L. thecatus, which together are the sister taxon of Nematoda; however, long branches and/or base composition bias could be responsible for this result. The monophyly of Ecdysozoa, molting organisms, was not supported by any of the analyses. This study represents the first mitochondrial genome of an acanthocephalan to be sequenced and will allow further studies of systematics, population genetics, and genome evolution.Reviewing Editor: Dr. Rafael Zardoya The entire genome sequence has been deposited with the GenBank Data Libraries under-accession number AY562383.     

Mitochondrial Genome of <Emphasis Type="Italic">Ciona savignyi</Emphasis> (Urochordata,Ascidiacea, Enterogona): Comparison of Gene Arrangement and tRNA Genes with <Emphasis Type="Italic">Halocynthia roretzi</Emphasis> Mitochondrial Genome

The complete nucleotide sequence of the urochordate Ciona savignyi (Ascidiacea, Enterogona) mitochondrial (mt) genome (14,737 bp) was determined. The Ciona mt genome does not encode a gene for ATP synthetase subunit 8 but encodes an additional tRNA^Gly gene (anticodon UCU), as is the case in another urochordate, Halocynthia roretzi (Ascidiacea, Pleurogona), mt genome. In addition, the Ciona mt genome encodes two tRNA^Met genes; anticodon CAT and anticodon TAT. The tRNA^Cys gene is thought to lack base pairs at the D-stem. Thus, the Ciona mt genome encodes 12 protein, 2 rRNA, and 24 tRNA genes. The gene arrangement of the Ciona mt genome differs greatly from those of any other metazoan mt genomes reported to date. Only three gene boundaries are shared between the Halocynthia and the Ciona mt genomes. Molecular phylogenetic analyses based on amino acid sequences of mt protein genes failed to demonstrate the monophyly of the chordates.     

An integrated physical and genetic map of the nematode<Emphasis Type="Italic"> Pristionchus pacificus</Emphasis>

The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.Communicated by G. Jürgens     

Putative genome donors ofArachis hypogaea (Fabaceae), evidence from crosses with synthetic amphidiploids

Chromosome pairing, pollen and pod fertility in hybrids between cultivated tetraploidArachis hypogaea and 15 synthetic amphidiploids from 8 diploid species (7 of the A genome and 1 of the B genome) of sect.Arachis have been utilized for the identification of putative genome donors in the evolution of cultivatedA. hypogaea. These results, in conjunction with evidence from morphological similarities, phytogeographical distribution and some phytochemical features, confirm the segmental amphidiploid origin ofA. hypogaea. A. batizocoi andA. duranensis are suggested as the donors of the B genome and the A genome respectively.     

Inter- and intra-genomic homology of the Brassica genomes: implications for their origin and evolution

In order to determine the homologous regions shared by the cultivated Brassica genomes, linkage maps of the diploid cultivated B. rapa (A genome, n = 10), B. nigra (B genome, n = 8) and B. oleracea (C genome, n = 9), were compared. We found intergenomic conserved regions but with extensitve reordering among the genomes. Eighteen linkage groups from all three species could be associated on the basis of homologous segments based on at least three common markers. Intragenomic homologous conservation was also observed for some of the chromosomes of the A, B and C genomes. A possible chromosome phylogenetic pathway based on an ancestral genome of at least five, and no more than seven chromosomes, was drawn from the chromosomal inter-relationships observed. These results demonstrate that extensive duplication and rearrangement have been involved in the formation of the Brassica genomes from a smaller ancestral genome.     

长爪栘[木衣]叶绿体基因组特征系统发育及密码子偏好性分析

长爪栘[木衣](Docynia longiunguis Q.Luo & J.L.Liu)是我国特有的栘[木衣]属植物,具有较高的食药用价值.对其叶绿体基因组进行分析,有助于阐明栘[木衣]属内的系统发育关系,为长爪栘[木衣]资源的开发利用及进一步研究奠定基础.结合其近缘种云南移[木衣]叶绿体基因组数据,在进行全序列比对后...     

Genomic groups,morphology, and sectional delimitation in EurasianElymus (Poaceae,Triticeae)

Seven tetraploid species ofElymus, viz.E. sibiricus, E. caninus, E. gmelinii, E. semicostatus, E. caucasicus, E. parviglume, andE. longearistatus subsp.canaliculatus, representing five sections were studied morphologically and used in interspecific hybridizations. The aim was to investigate whether the present sectional delimitation of the genus was in agreement with genomic data and if there was a correlation between genome constitution and morphology. The study revealed: (i) further information on the genomic affinities between the different species, (ii) that there is no congruence between genome constitution of the species and current sectional delimitation, and (iii) that there is a correlation between genome constitution and morphology in the palea apex shape and in the size of cilia of the palea.     

Inferred chromosome morphology of the ancestral genome ofTriticum

The lengths of the A, B, and D genomes of common wheat,Triticum aestivum, were measured from the karyotype. Relative to the B genome, standardized as length 1.000, the lengths of the A and D genomes were 0.835 and 0.722, respectively. The lengths of the chromosome arms in the A and D genomes were then multiplied by the appropriate constants so that the total lengths of each genome also equalled 1.000. These calculations revealed that homoeologous chromosomes in wheat, with a few exceptions, have similar sizes and arm ratios. The arm lengths of the three homoeologues in each homoeologous group were then averaged. These average chromosomes turned out to be remarkably similar, in size and arm ratio, to their homoeologues in the E genome ofElytrigia elongata. This evidence and data on cross-compatibility and morphological characteristics suggested that the genusTriticum is a result of adaptive radiation from the perennial genusElytrigia, specifically from the complex of species possessing the E genome or one closely related to it.     

Amplification and dispersion of repeated DNA sequences in theTriticeae

Four representatives of a family of dispersed repetitive sequences which were prominent and dispersed in the E genome ofThinopyrum elongatum but poorly represented in wheat, were studied in detail. The 1.4kb sequences were present both as part of tandem and more complex arrays and appeared to have resulted from repeated amplification of the sequence and their dispersion throughout the genome. Subcloning of sections of the 1.4 kb sequences resulted in probes which improved the resolution of the E genome from the genomes in wheat and enabled identification of single E genome chromosomes introduced into wheat. The generality of these types of sequences in the tribeTriticeae was confirmed by isolating analogous sequences from the R (rye,Secale cereale), V (Dasypyrum villosum), and N (Psathyrostachys juncea) genomes. — The cloned repetitive sequences from the R, V, and N genomes each showed characteristic fluctuations in amount within the grasses examined in addition to being virtually absent from wheat. It is thus possible that these sequences may provide useful taxonomic indicators for establishing relationships within theTriticeae, as well as valuable probes for tracing alien chromatin introduced into wheat.     

Interspecies distribution of abundant DNA sequences inLilium

Summary The most abundantly repeated sequences in the very large genomes ofLilium henryi andLilium longiflorum have been characterized. DNA reannealed by a Cot of 1 Ms, which specifies the half reannealing point of sequences repeated 18–19,000 times per genome, was used to probe genomic libraries and restriction digests of each species. InL. henryi this fraction includes 2.2% of the genome, wheareas 9.7% of theL. longiflorum genome reanneals by Cot 1. The most abundant repeat identified was thedel retrotransposon. This is at least three times more common in the genome ofL. longiflorum than inL. henryi where it occurs in excess of 13,000 copies. It was also detected in the genomes of 12 otherLilium species examined. None of these have more copies ofdel per genome thanL. longiflorum, some having at least 100-fold fewer. The phylogenetic distribution ofdel across the genus suggests repeated, sporadic amplification events. Another very abundant repeat was identified as 5S ribosomal DNA (rDNA). In this case many more copies were present in the genome ofL. henryi than inL. longiflorum. The number of 5S rDNA copies also varied markedly across other members of the genus with a distribution unrelated todel.     

Asynchronous meiotic rhythm as the cause of selective chromosome elimination in an interspecific <Emphasis Type="Italic">Brachiaria</Emphasis> hybrid

This paper reports the occurrence of chromosome elimination during microsporogenesis in an interspecific hybrid between a sexual diploid accession (SEX) of Brachiaria ruziziensis (2n=2x=18) and an apomictic tetraploid accession (APO) of B. brizantha (2n=4x=36). Meiosis was very abnormal in the triploid hybrid (2n=3x=27); we observed a distinct asynchrony from metaphase I to the end of meiosis. The APO and the SEX genomes did not show the same meiotic rhythm. When the former, with nine bivalents, was in metaphase I, the nine SEX univalents were not yet aligned; when the latter reached the plate, the APO genome was already in anaphase. In subsequent stages, the APO genome had reached the poles while the SEX was undergoing sister-chromatid segregation. As the SEX genome always remained temporally behind, it gave rise to one extra-nucleus in each pole. In the second division, the behavior was the same but anaphase II did not occur for the SEX genome, and only one extra-nucleus was observed in each cell in telophase II. Chromosome elimination for the SEX genome ranged from partial to total. The importance of these findings with respect to Brachiaria breeding programmes is discussed.