THE CYTOLOGY AND PHYLOGENETICS OF THE DIPLOID SPECIES OF GOSSYPIUM

Meiotic chromosome behavior of 11 inter-genomic hybrids of Gossypium (2n = 26) were investigated. Per cell univalent frequencies at meiotic metaphase I in these hybrids were: A genome × Cgenome—G. herbaceum × sturtianum, 10.53; G. herbaceum × australe, 18.05. A genome × E genome—G. smnalense × arboreum, 21.82. B genome × C genome—G. anomalum × sturtianum, 9.23; G. anomalum × australe, 13.11. B genome × D genome—G. anomalum × klotzschianum, 17.45; G. anomalum × raimondii, 18.83. C genome × D genome—G. robinsonii × davidsonii, 12.77; G. sturtianum (armourianum × thurberi), 8.63. C genome × E genome—G. somalense × australe, 23.78; G. somalense × bickii, 25.58. Trivalent and quadrivalent frequencies were relatively high for those hybrids involving a C genome species, indicating that a reciprocal translocation differentiates the C genome from the A, B, D, and E genomes. The results of this study and the data of similar studies cited from the literature on Gossypium cytogenetics are discussed relative to the phylogenetics and evolution of the major (genome) groups of Gossypium and their constituent taxa.     

Genome Re-duplication and Irregular Segregation Occur During the Cell Cycle of Entamoeba histolytica

Heterogeneity of genome content is commonly observed in axenic cultures of Entamoeba histolytica. Cells with multiple nuclei and nuclei with heterogenous genome contents suggest that regulatory mechanisms that ensure alternation of DNA synthesis and mitosis are absent in this organism. Therefore, several endo-reduplicative cycles may occur without mitosis. The data also shows that unlike other endo-reduplicating organisms, E.histolytica does not undergo a precise number of endo-reduplicative cycles. We propose that irregular endo-reduplication and genome partitioning lead to heterogeneity in the genome content of E.histolytica trophozoites in their proliferative phase. The goal of future studies should be aimed at understanding the mechanisms that are involved in (a) accumulation of multiple genome contents in a single nucleus; (b) genome segregation in nuclei that contain multiple genome contents and (c) maintenance of genome fidelity in E. histolytica.     

The origins of the genomes of Triticum biunciale,t. ovatum,t. neglectum,t. columnare,and t. rectum (poaceae) based on variation in repeated nucleotide sequences

The origins of the genomes of allotetraploid species Triticum biunciale, T. ovatum, T. neglectum, and T. columnare, and allohexaploid T. rectum were investigated by examining the presence of specific restriction fragments of repeated nucleotide sequences in DNAs of the polyploid species. The restriction fragments were detectable either in a single diploid Triticum species (unique characters) or a group of diploid species (unique shared characters). The analysis showed that Triticum biunciale and T. ovatum are closely related. In both species, one pair of genomes is closely related to the genome of T. umbellulatum and the other is a modified genome of T. comosum. The same genome formula, UUM°M°, is proposed for T. biunciale and T. ovatum. Potential reasons for the modification of the M° genome are discussed. Triticum neglectum and T. columnare are also closely related to each other and have the same genomes. They share the U genome with T. biunciale and T. ovatum, but their second pair of genomes is unrelated to the M° genome. No relationship was found of this genome to a genome of any extant diploid species of Triticum or any phylogenetic lineage leading to the extant diploid species. This unknown genome is designated X'.∗∗∗ The proposed genome formula for T. neglectum and T. columnare is UUX'X'∗∗∗. Hexaploid T. rectum originated from hybridization of one of the tetraploid species with the formula UUX'X', likely T. neglectum, with T. uniaristatum (genome N), and its genome formula is UUX'X'NN.     

Nucleo-cytoplasmic incompatibility in cybrid plants possessing an Atropa genome and a Nicotiana plastome.

Summary Twenty-nine cybrids possessing an Atropa belladonna nuclear genome and a Nicotiana tabacum plastome were selected from two independent protoplast fusion experiments. In contrast to the previously described reciprocal, green and fertile cybrids with a Nicotiana nuclear genome and an Atropa plastome (Kushnir et al. 1987), the plants obtained were totally chlorophyll-deficient. An Atropa nuclear genome and a Nicotiana plastome from these chlorophyll-deficient cybrids were combined with an Atropa or a Scopolia plastome and a Nicotiana nuclear genome, respectively, in control fusion experiments. All of these nuclear genome/plastome combinations gave rise to normal, green plants. Therefore, we conclude that an N. tabacum plastome is incompatible with an A. belladonna nuclear genome.     

Phylogenetic inferences in Avena based on analysis of FL intron2 sequences

The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species. The Avena FL int2 is rather long, and high levels of variation in length and sequence composition were found. Evidence for more than one copy of the FL int2 sequence was obtained for both the A and C genome groups, and the degree of divergence of the A genome copies was greater than that observed within the C genome sequences. Phylogenetic analysis of the FL int2 sequences resulted in topologies that contained four major groups; these groups reemphasize the major genomic divergence between the A and C genomes, and the close relationship among the A, B, and D genomes. However, the D genome in hexaploids more likely originated from a C genome diploid rather than the generally believed A genome, and the C genome diploid A. clauda may have played an important role in the origination of both the C and D genome in polyploids.     

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.     

Flow cytometric analysis of nuclear DNA content in Musa

 Nuclear genome size variation was studied in Musa acuminata (A genome), Musa balbisiana (B genome) and a range of triploid clones differing in genomic constitution (i.e. the relative number of A and B genomes). Nuclear DNA content was estimated by flow cytometry of nuclei stained by propidium iodide. The A and B genomes of Musa differ in size, the B genome being smaller by 12% on average. No variation in genome size was found among the accessions of M. balbisiana (average genome size 537 Mbp). Small, but statistically significant, variation was found among the subspecies and clones of M. acuminata (ranging from 591 to 615 Mbp). This difference may relate to the geographical origin of the individual accessions. Larger variation in genome size (8.8%) was found among the triploid Musa accessions (ranging from 559 to 613 Mbp). This variation may be due to different genomic constitutions as well as to differences in the size of their A genomes. It is proposed that a comparative analysis of genome size in diploids and triploids may be helpful in identifying putative diploid progenitors of cultivated triploid Musa clones. Statistical analysis of data on genome size resulted in a grouping which agreed fairly well with the generally accepted taxonomic classification of Musa. Received: 11 May 1998 / Accepted: 29 September 1998     

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.     

CHLOROPLAST DNA EVIDENCE FOR GENOME DIFFERENTIATION IN WILD POTATOES (SOLANUM SECT. PETOTA: SOLANACEAE)

Chloroplast DNA restriction site analysis has been used to test Hawkes's phylogenetic interpretations of the genomic data in Solanum sect. Petota. Hawkes hypothesized a diploid (2n = 24) origin of the tuber-bearing members of this group (subsection Potatoe) in Mexico and Central America (as a B genome) with later migrations and evolution to an A genome in South America, later followed by a return migration of the A genome to Mexico and Central America with A × B hybridizations and polyploidizations to produce ser. Longipedicellata (4x) and Demissa (6x). Our results provide partial support for this hypothesis by demonstrating the paraphyletic and primitive nature of the B genome species group, and the monophyletic and derived nature of all A genome and A × B genome species, including S. verrucosum, a hypothesized A genome progenitor of ser. Demissa. Thus, the Mexican and Central American polyploid species must have obtained their cytoplasm from the A genome. However, our results question the Stellata/Rotata hypothesis of Hawkes and the taxonomic placement of S. chomatophilum in ser. Conicibaccata.     

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).     

A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?

Genome sizes vary widely among species, but comprehensive explanations for the emergence of this variation have not been validated. Lynch and Conery (2003) hypothesized that genome expansion is maladaptive, and that lineages with small effective population size (N_e) evolve larger genomes than those with large N_e as a consequence of the lowered efficacy of natural selection in small populations. In addition, mating systems likely affect genome size evolution via effects on both N_e and the spread of transposable elements (TEs). We present a comparative analysis of the effects of N_e and mating system on genome size evolution in seed plants. The dataset includes 205 species with monoploid genome size estimates (corrected for recent polyploidy) ranging from 2Cx = 0.3 to 65.9 pg. The raw data exhibited a strong positive relationship between outcrossing and genome size, a negative relationship between N_e and genome size, but no detectable N_e× outcrossing interaction. In contrast, phylogenetically independent contrast analyses found only a weak relationship between outcrossing and genome size and no relationship between N_e and genome size. Thus, seed plants do not support the Lynch and Conery mechanism of genome size evolution. Further work is needed to disentangle contrasting effects of mating systems on the efficacy of selection and TE transmission.     

Unique genome replication mechanism of the archaeal virus AFV1

The exceptional genomic content and genome organization of the Acidianus filamentous virus 1 (AFV1) that infects the hyperthermophilic archaeon Acidianus hospitalis suggest that this virus might exploit an unusual mechanism of genome replication. An analysis of replicative intermediates of the viral genome by two‐dimensional (2D) agarose gel electrophoresis revealed that viral genome replication starts by the formation of a D‐loop and proceeds via strand displacement replication. Characterization of replicative intermediates using dark‐field electron microscopy, in combination with the 2D agarose gel electrophoresis data, suggests that recombination plays a key role in the termination of AFV1 genome replication through the formation of terminal loops. A terminal protein was found to be attached to the ends of the viral genome. The results allow us to postulate a model of genome replication that relies on recombination events for initiation and termination.     

The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs

The complete nucleotide sequence (501,020 bp) of the mitochondrial genome from cytoplasmic male-sterile (CMS) sugar beet was determined. This enabled us to compare the sequence with that previously published for the mitochondrial genome of normal, male-fertile sugar beet. The comparison revealed that the two genomes have the same complement of genes of known function. The rRNA and tRNA genes encoded in the CMS mitochondrial genome share 100% sequence identity with their respective counterparts in the normal genome. We found a total of 24 single nucleotide substitutions in 11 protein genes encoded by the CMS mitochondrial genome. However, none of these seems to be responsible for male sterility. In addition, several other ORFs were found to be actively transcribed in sugar beet mitochondria. Among these, Norf246 was observed to be present in the normal mitochondrial genome but absent from the CMS genome. However, it seems unlikely that the loss of Norf246 is causally related to the expression of CMS, because previous studies on mitochondrial translation products failed to detect the product of this ORF. Conversely, the CMS genome contains four transcribed ORFs (Satp6presequence, Scox2-2 , Sorf324 and Sorf119) which are missing from the normal genome. These ORFs, which are potential candidates for CMS genes, were shown to be generated by mitochondrial genome rearrangements.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by R. Hagemann     

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.     

不同处理方法对肺炎链球菌基因组提取的影响

为了获得简便、高效的提取肺炎链球菌基因组DNA方法,分别采用不同处理方法(溶菌酶法和脱氧胆酸钠(DOC)法)、不同处理时间对8株不同血清型的肺炎链球菌进行破壁,同时菌株采用不同培养时间进行基因组的提取,提取基因组后利用紫外分光光度计测定样品中DNA的浓度和纯度以及琼脂糖凝胶电泳检测基因组DNA的质量。结果表明,菌株培养12~16 h、质量分数1%DOC处理2 h能提取出高质量的肺炎链球菌基因组DNA。该方法提取的肺炎链球菌基因组DNA具有质量高、完整性好的优点,为肺炎链球菌全基因组序列的测定提供了前提条件。     

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

Background  

Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.     

Quantification and characterization of nuclear genomes in commercial red seaweeds: Gracilariales and Gelidiales

Nuclear genome profiles were developed for representative species of the Gelidiales and Gracilariales using information from present and previous studies of cytogenetics, cytophotometry and DNA reassociation kinetics. Results indicate that species of Gracilaria and Gracilariopsis are characterized by distinct chromosome complements of n = 24 and n = 32, respectively, a narrow range of small genome sizes (2C = 0.35–0.45 pg) and a wide range of values for repeated and unique genome sequences. In contrast, the Gelidiales investigated are characterized by a wide range of chromosome complements, n = 6–29, a wider range of genome sizes (2C = 0.42–0.68 pg) and a large proportion of unique genome sequences. Nuclear genome sizes for species of the Gelidiales and Gracilariales are compared with estimates of other red algal orders including the Bangiales, Ceramiales and Gigartinales.     

Genome-wide identification of NBS-encoding resistance genes in <Emphasis Type="Italic">Brassica rapa</Emphasis>

Nucleotide-binding site (NBS)-encoding resistance genes are key plant disease-resistance genes and are abundant in plant genomes, comprising up to 2% of all genes. The availability of genome sequences from several plant models enables the identification and cloning of NBS-encoding genes from closely related species based on a comparative genomics approach. In this study, we used the genome sequence of Brassica rapa to identify NBS-encoding genes in the Brassica genome. We identified 92 non-redundant NBS-encoding genes [30 CC-NBS-LRR (CNL) and 62 TIR-NBS-LRR (TNL) genes] in approximately 100 Mbp of B. rapa euchromatic genome sequence. Despite the fact that B. rapa has a significantly larger genome than Arabidopsis thaliana due to a recent whole genome triplication event after speciation, B. rapa contains relatively small number of NBS-encoding genes compared to A. thaliana, presumably because of deletion of redundant genes related to genome diploidization. Phylogenetic and evolutionary analyses suggest that relatively higher relaxation of selective constraints on the TNL group after the old duplication event resulted in greater accumulation of TNLs than CNLs in both Arabidopsis and Brassica genomes. Recent tandem duplication and ectopic deletion are likely to have played a role in the generation of novel Brassica lineage-specific resistance genes.     

Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley

Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third‐generation sequencer (PacBio), we de novo assembled a 4.84‐Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59‐Gb sequence to seven chromosomes. Of the 46,787 annotated ‘high‐confidence’ genes, 31 564 were validated by RNA‐sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low‐diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.