Diversity and evolution of four dispersed repetitive DNA sequences in the genus Secale

We present the first characterization of 360 sequences in six species of the genus Secale of both cultivated and wild accessions. These include four distinct kinds of dispersed repetitive DNA sequences named pSc20H, pSc119.1, pSaO5(411), and pSaD15(940) belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5(411)-like sequences became shorter mainly because of the deletion of a trinucleotide tandem repeating unit, the pSc20H-like sequences displayed apparent homogenization in cultivated rye, and the second intron of Revolver became longer. In addition, the pSc20H-, pSc119.1-, and pSaO5(411)-like sequences cloned from wild rye and cultivated rye could be divided into two large clades. No single case of the four kinds of repetitive elements has been inherited by each Secale accession from a lone ancestor. It is reasonable to consider the vertical transmission of the four repetitive elements during the evolution of the genus Secale. The pSc20H- and pSaO5(411)-like sequences showed evolutionary elimination at specific chromosomal locations from wild species to cultivated species. These cases imply that different repetitive DNA sequences have played different roles in the chromosome development and genomic evolution of rye. The present study adds important information to the investigations dealing with characterization of dispersed repetitive elements in wild and cultivated rye.     

Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history

Retrotransposons are abundant in higher plant genomes. Although retrotransposons associated with plant genes have been identified, little is known about their evolutionary conservation at the level of species and subspecies. In the present study, we investigated the phylogenetic distribution of long terminal repeat (LTR) retrotransposon, long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) insertions in six genes in 95 cultivated and wild rice genotypes. These six genes are likely to be functional based on nonsynonymous (Ka) to synonymous (Ks) substitution ratios which were found to be significantly <1. Different conservation patterns of these retrotransposons in genes were observed in cultivated and wild rice species. Four out of seven retrotransposon insertions appear to predate the ancestral Oryza AA genome. Two of these insertions in genes 4 and 5 occurred early in the evolutionary history of Oryza. Two retrotransposon insertions in gene 1 arose after the divergence of Asian cultivated rice from its wild ancestor. Furthermore, the retrotransposon insertion in gene 3 appears to have occurred in the ancestral lineage leading to temperate japonicas. Conservation of retrotransposon insertions in genes in specific groups, species, and lineages might be related to their specific function.     

The effects of artificial selection on sugar metabolism and transporter genes in grape

Sugar content is a key feature of grape quality. The sugar content of grapes has been significantly improved after nearly a thousand years of artificial selection. However, the mechanism underlying the changes in the grape sugar content during the process of artificial selection remains largely unknown although several genes involved in sugar metabolism and transportation in grape have been identified. In this study, the genomes of 13 wild Vitis species and 14 cultivated Vitis vinifera accessions were resequenced to 2–5 X depth using the Illumina Hiseq2000 platform. Genetic variation of 138 genes involved in sugar biosynthesis and transport was investigated, and 7,690 and 12,717 single nucleotide polymorphisms/insertions and deletions (SNPs/InDel) were identified within the cultivated V. vinifera and wild Vitis species, respectively. The percentages of SNPs/InDels were 0.93 and 1.54 % in cultivated and wild species, respectively, and the wild Vitis species had 1.65-fold more SNPs/InDels than the cultivated V. vinifera. Moreover, the distribution of SNPs/InDels in gene regions was also investigated. Eight genes (HT4, PPFTK4, PPFTK6, PMT3, SPS1, HT8, HT15, SUSy1) showed low level of allelic diversity in cultivated species, suggesting they might have undergone purifying selection during the domestication process of grapes. Our genome DNA resequencing data provided a valuable resource for analyzing the effects of artificial selection on trait-related pathways in grape. The result that eight genes showed lower level of DNA variation in cultivated species than in wild species will be very helpful in understanding sugar accumulation in grapes.     

Soybean Recombination Sites are Present as Dispersed Segments in Arabidopsis and Liverwort Mitochondrial DNA

In previous studies we have shown that recombination across a 299-bp interspersed sequence accounts for the diversity of the mitochondrial genome in wild and cultivated soybeans. In this study, a computer-assisted survey of databases was performed using sequences of the repeat and its neighboring regions as query sequences. The sequences of soybean were found to be present as many short segments that include repeated sequences in the mitochondrial genomes of Arabidopsis and liverwort. Taken together with the results of a DNA gel-blot analysis, this suggests that the soybean sequences were found to have originated during land plant evolution and are present as small-interspersed segments in many taxa of land plants.     

Saccharum species as horticultural classes

 Sugarcane, commonly referred to as Saccharum officinarum, is currently divided into six species, two of them are wild and four exist only in cultivation. The two wild species and three of the cultivated ones are interfertile and have produced the interspecific hybrids that constitute the sugarcane of commerce. All species are represented by wide ranges of intergrades preserved as clones through vegetative propagation. Species are separated by variable floral characters, sugar content, chromosome numbers and epidermal hair groups. Floral characteristics are sometimes useful with clones that flower, sugar is present in widely overlapping ranges and is highly influenced by environment, chromosome numbers range from 36 to 170 in the genus and range widely within species, and some epidermal hair groups are more quantitative than qualitative. Molecular techniques show that Saccharum spontaneum is distinctly different from the other species in cytoplasmic DNA, and cluster analyses of nuclear DNA support the difference. Not only are the species interfertile but chromosomal pairing and recombination have been demonstrated, as has the possibility that some Saccharum species are hybrids of others. Taken together, these observations suggest that there is little basis for the present separation and that the six species should more properly consist of two: one being S. spontaneum, based on molecular data, and the other S. officinarum including the other four species and all interspecific hybrids. Received: 20 December 1997 / Accepted: 5 June 1998     

Chromosomal study of lettuce and its allied species (Lactuca spp., Asteraceae) by means of karyotype analysis and fluorescence in situ hybridization

In this study, in addition to the karyotype analysis, the chromosomal distributions of 5 S and 18 S rDNAs, and the Arabidopsis-type (T3AG3) telomeric sequences were detected by means of fluorescence in situ hybridization (FISH) to promote the information of chromosomal organization and evolution in the cultivated lettuce and its wild relatives, L. sativa, L. serriola, L. saligna and L. virosa. The karyotype analysis revealed the dissimilarity between L. virosa and the remaining species. In all four Lactuca species studied, one 5 S rDNA and two 18 S rDNA loci were detected. The simultaneous FISH of 5 S and 18 S rDNAs revealed that both rDNA loci of L. sativa, L. serriola and L. saligna were identical, however, that of L. virosa was different from the other species. These analyses indicate the closer relationships between L. sativa/L. serriola and L. saligna rather than L. virosa. Arabidopsis-type telomeric sequences were detected at both ends of their chromatids of all chromosomes not in the other regions. This observation suggests the lack of telomere-mediated chromosomal rearrangements among the Lactuca chromosomes.     

Monosomic addition lines of Beta corolliflora Zoss in sugar beet: cytological and molecular-marker analysis

Beta corolliflora is a wild relative of sugar beet (Beta vulgaris) with 2n=4x=36 chromosomes. Monosomic addition lines (2n=19) of B. corolliflora in B. vulgaris were identified from backcross progenies between triploid hybrids (genome constitution VVC) and sugar beet. They were characterized by DNA-fingerprinting using nine different B. corolliflora-specific repetitive sequences as probes and by fluorescence in situ hybridization (FISH) using two B. corollifora specific sequences and two rDNA probes. Unique banding patterns obtained after genomic Southern hybridization enabled the classification of monosomic addition lines into 11 clusters, three of which proved to have a wild beet chromosome fragment in addition to the sugar beet chromosomes as revealed by FISH. Repetitive sequences pBC216 and pBC1416 were found to be present only on wild beet chromosomes IV and V. Chromosomes I and IV were found to carry genes for 18S and 5S rRNA, respectively. An idiogram of B. corolliflora was established in the triploid VVC hybrid on the basis of chromosome size and FISH. Eight B. corolliflora addition lines could be unequivocally identified by Southern hybridization and FISH, one addition line carrying the missing wild beet chromosome is probably not viable under greenhouse conditions. The monosomic addition lines will serve as a bridge for transferring genes from wild species to sugar beet and will help to uncover genetic relationships between species of the genus Beta.     

药用野生稻复合体ITS1和ITS2序列变异及其系统进化分析

通过PCR扩增并测序分析稻属药用野生稻复合体5个野生稻种基因组完整的ITS区及5.8S区,并与栽培稻ITS序列进行比较,构建分子系统进化树,探讨了稻属药用野生稻复合体内不同种间的亲缘关系和系统进化.结果表明,ITS1和ITS2均有较高的G/C含量,ITS1序列的长度多态性相对较高,ITS2序列的碱基突变频率较高.药用野生稻和高秆野生稻亲缘关系很近,而与栽培稻亲缘关系较远;短药野生稻、斑点野生稻、澳洲野生稻与药用野生稻亲缘关系渐近.处于进化的过渡阶段.     

荞麦属种间13S球蛋白基因序列比较研究

荞麦13S球蛋白是荞麦种子中的一类主要贮藏蛋白。本研究选用荞麦属植物甜荞栽培种及其野生类型、苦荞栽培种及其野生类型、毛野荞、左贡野荞、细柄野荞和硬枝万年荞6个种共44份材料,进行PCR特异性扩增、测序得到荞麦13S球蛋白基因的保守片段序列。对序列进行差异分析,结果发现44份供试材料13S球蛋白基因片段的285个排列位点中不变位点为24个,多态性位点S为261个(含简约信息位点数198个和单型可变位点63个),序列总突变位点Eta为503个。野生甜荞种内13S球蛋白基因序列差异明显高于栽培甜荞,但野生苦荞种内13S球蛋白基因序列差异仅稍高于栽培苦荞。推测其一方面可能与繁殖方式有关,另一方面可能与荞麦驯化过程中通常只有少数野生型群体被驯化有关。系统聚类分析发现栽培甜荞与野甜荞亲缘关系近,与左贡野荞亲缘关系次之;栽培苦荞与野苦荞亲缘关系近,与毛野荞亲缘关系次之;细柄野荞和硬枝万年荞的13S蛋白基因片段序列差异较小,说明其亲缘关系较近。上述结果为荞麦属种间遗传多样性与进化关系研究提供了理论依据。     

ITS1 Sequences of Nuclear Ribosomal DNA in Wild Rices and Cultivated Rices of China and Their Phylogenetic Implications

he first internal transcribed spacer (ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3%to 72.7%. In pairwise comparison among the five taxa, sequence site divergence ranged from 1.5 % to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well-resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) of the genus Oryza.     

Isolation and characterization of S genome specific sequences from Aegilops sect. sitopsis species.

Three S genome specific sequences were isolated from Aegilops sect. sitopsis species using different experimental approaches. Two clones, UTV86 and UTV39, were isolated from a partial genomic library obtained from DNA of Aegilops sharonensis, whereas a third clone, UTV5, was isolated from Aegilops speltoides. The three clones were characterized by sequencing, analysis of methylation, and sequence organization and abundance in some Aegilops and Triticum species. The clones UTV39 and UTV5 belong to the same family of tandem repeated sequences and showed high homology with a sequence already present in nucleotide databases. The UTV86 clone from Ae. sharonensis corresponded to an interspersed low frequency repeated sequence and did not show any significant homology with reported sequences. Southern hybridization experiments, using the cloned sequences as probes, detected polymorphism in the restriction patterns of all the five Aegilops species in section sitopsis. Aegilops speltoides showed the most divergent hybridization pattern. A close relationship was detected between the S genome of Ae. speltoides and the G genome of the wild Triticum timopheevii. In situ hybridization revealed a telomeric and (or) subtelomeric location of the sequences UTV39 and UTV5.     

中国野生稻及栽培稻核糖体DNA第一转录间隔区序列分析及其系统学意义

用 PCR技术从产于我国的 3种野生稻和亚洲栽培稻的 2个亚种中特异地扩增和测序了 r DNA的第一转录间隔区。普通野生稻 (Oryza rufipogon)、药用野生稻 (O.officinalis)、疣粒野生稻 (O.granu-lata)和栽培稻的两个亚种 (O.sativa ssp.indica,O.sativa ssp.japonica)的 ITS1序列为 1 93bp、1 94bp、2 1 8bp、1 94bp和 1 94bp,它们的 G/ C含量为 69.3%～ 72 .7% ,序列中位点趋异率为 1 .5%～ 1 0 .6%。序列的相似性比较和简约性分支分析的结果表明 ,普通野生稻与栽培稻的两个亚种之间的亲缘关系最为密切 ;药用野生稻与普通野生稻和与栽培稻的两个亚种的相似性都为 82 % ,说明它与 AA基因组有一定的亲缘关系 ;疣粒野生稻与普通野生稻、药用野生稻和栽培稻两个亚种的亲缘关系相对较远 ,它在稻属中可能是一个系统地位较独特的类群。以 ITS1序列构建的 3种野生稻和 2个栽培稻亚种的系统发育关系与前人用同工酶、叶绿体 DNA、线粒体 DNA和核 DNA资料重建的稻属的系统发育关系基本一致     

GIS-based characterization of the geographic distributions of wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea (Anacardiaceae)

Humans are having a profound impact on the geographic distributions of plant populations. In crop species, domestication has been accompanied by the geographic expansion of cultivated populations relative to their wild ancestors. We used a geographical information system (GIS)-based approach to investigate differences in the environmental factors characterizing the geographic distributions of cultivated and wild populations of the Mesoamerican fruit tree Spondias purpurea. Locality data for 86 cultivated and 28 wild S. purpurea populations were used in conjunction with environmental data layers and Maxent, a maximum entropy application for predicting species distributions. Interpredictivity analyses and principal components analysis revealed that the predicted distribution of wild S. purpurea is nested within the cultivated distribution and that the ecological niche (defined by environmental characteristics) of cultivated S. purpurea has expanded relative to that of wild populations. Significant differences between wild and cultivated populations were detected for five environmental variables, corresponding to the expansion of S. purpurea during the domestication process from its native habitat in the Mesoamerican tropical dry forests into less seasonal habitats. These data suggest that humans have altered the range of habitats occupied by cultivated S. purpurea populations relative to their wild progenitors.     

RAPD markers linked to the nuclear gene from Triticum timopheevii that confers compatibility with Aegilops squarrosa cytoplasm on alloplasmic durum wheat.

Alien cytoplasms cause a wide range of phenotypic alterations in the nucleus-cytoplasm (NC) hybrids in the Triticeae. Nuclear genomes of timopheevii wheat (Triticum timopheevii and Triticum araraticum) are fully compatible with the cytoplasm of Aegilops squarrosa, while those of a majority of emmer or durum wheat cultivars and more than half the wild emmer wheats are incompatible, and a maternal 1D chromosome is required to restore seed viability and male fertility in the NC hybrids. A euploid NC hybrid of Triticum durum cv. Langdon with Ae. squarrosa cytoplasm produced by introgressing the NC compatibility (Ncc) gene from T. timopheevii was used to identify random amplified polymorphic DNA (RAPD) markers linked to it. After a survey of 200 random decamer primers, four markers were selected, all of which were completely linked in 64 individuals of a SB8 mapping population. One marker was derived from a single locus, while three others were from interspersed repetitive sequences. Also, the hybrid chromosomes and those of the parental T. durum had identical C-banding patterns. RAPD-PCR analysis of 65 accessions from wild and cultivated tetraploid wheat species showed the exclusive presence of the markers in timopheevii wheat. In conclusion, the chromosomal region flanking Ncc of T. timopheevii is highly conserved in the genome of this group of tetraploid wheats.     

Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species.

Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum, Ideonella, Enterobacter, and Azospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and (15)N(2) gas incorporation assays. Therefore, we conclude that Herbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis.     

Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

The origin of cultivated tree peonies, known as the ‘king of flowers'' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.     

Comparative analysis of superfamilies of NBS-encoding disease resistance gene analogs in cultivated and wild apple species

Eleven distinct families of resistance gene analogs (RGAs) with the characteristic nucleotide-binding sequence (NBS) were identified in two wild apple species, Malus prunifolia and M. baccata, and two cultivated apple cultivars, M. domestica cv. Fuji and M. domestica cv. Hong-ok, using PCR approaches with degenerate primers based on two conserved motifs of known NBS-LRR resistance genes. These RGA families were found to be represented in all the apple species tested, including wild and cultivated species. However, their sequences are very divergent from each other. Furthermore, the low level of recombination detected within their RGA families supports the idea that the evolution of NBS-encoding sequences in apple species involves the gradual accumulation of mutations. Despite the high diversity of the RGA families found in all apple species, the apparent lack of differentiation between wild and cultivated forms suggests that other factors, such as the capacity to tolerate pathogens, might play an important role in the survival of wild-type species.     

Clustered and interspersed repetitive DNA sequences in four amphibian species with different genome size.

We have compared the amount of clustered and interspersed repetitive sequences in the genome of four Amphibia with different DNA contents per haploid nucleus: two Anura (Xenopus laevis, 3 pg and Bufo bufo, 7 pg) and two Urodela (Triturus cristatus, 23 pg and Necturus maculosus, 52 pg). High molecular weight DNA of the four species was denatured and reassociated to the same Cot in order to obtain duplex sequences with a similar reiteration frequency. Single-stranded DNA was digested off with the Aspergillus S1 nuclease. DNA was then fractionated according to the molecular weight through an agarose A-50 column. We found that the amount of long repetitive sequences is roughly proportional to the genome size in the four species, while the number of short (about 300 base pairs) repetitive sequences is increased many-fold in the species with the larger DNA content, both in Anura and in Urodela.     

Domestication Syndrome in Caimito (<Emphasis Type="Italic">Chrysophyllum cainito</Emphasis> L.): Fruit and Seed Characteristics

Domestication Syndrome in Caimito ( Chrysophyllum cainito L.): Fruit and Seed Characteristics: The process of domestication is understudied and poorly known for many tropical fruit tree crops. The star apple or caimito tree (Chrysophyllum cainito L., Sapotaceae) is cultivated throughout the New World tropics for its edible fruits. We studied this species in central Panama, where it grows wild in tropical moist forests and is also commonly cultivated in backyard gardens. Using fruits collected over two harvest seasons, we tested the hypothesis that cultivated individuals of C. cainito show distinctive fruit and seed characteristics associated with domestication relative to wild types. We found that cultivated fruits were significantly and substantially larger and allocated more to pulp and less to exocarp than wild fruits. The pulp of cultivated fruits was less acidic; also, the pulp had lower concentrations of phenolics and higher concentrations of sugar. The seeds were larger and more numerous and were less defended with phenolics in cultivated than in wild fruits. Discriminant Analysis showed that, among the many significant differences, fruit size and sugar concentration drove the great majority of the variance distinguishing wild from cultivated classes. Variance of pulp phenolics among individuals was significantly higher among wild trees than among cultivated trees, while variance of fruit mass and seed number was significantly higher among cultivated trees. Most traits showed strong correlations between years. Overall, we found a clear signature of a domestication syndrome in the fruits of cultivated caimito in Panama.     

Chromosomal localization and polymorphisms of ribosomal DNA in oat (Avena spp.).

The 17S/5.8S/26S ribosomal DNA (rDNA) sequences were mapped to the three satellited (SAT) chromosomes in the common hexaploid cultivated oat Avena sativa (2n = 6x = 42, AACCDD genomes). In situ hybridization and Southern hybridization of maize and (or) wheat rDNA probes to DNA from nullisomics derived from the cultivar 'Sun II' allowed the placement of rDNA sequences to the physical chromosomes. A restriction map was produced for the rDNA sequences of 'Sun II' using a maize probe from the transcribed region of the 17S/26S rDNA repeat. The set of rDNA repeats on SAT 2 of 'Sun II' possesses a 10.5-kb EcoRI fragment not found in the rDNA repeats of SAT 1 and SAT 8. This 10.5-kb fragment results from the absence of an EcoRI site in the intergenic spacer (IGS) of SAT 2 repeats. Extensive polymorphisms were demonstrated for three hexaploid Avena species, namely, the Mediterranean-type cultivated oat A. byzantina and the wild species A. sterilis and A. fatua. However, geographically diverse A. sativa cultivars displayed little rDNA variation. In contrast with all of the A. sativa cultivars examined, the A. sterilis accessions generally lacked the 10.5-kb EcoRI fragment. The results support the hypothesis that A. sativa accessions descend from a limited ancestral cultivated population. The rDNA polymorphisms are attributed to differences in lengths and restriction sites of the IGS.