西瓜与近缘种亲缘关系的比较基因组原位杂交分析

物种间亲缘关系的研究是杂交育种的理论基础,野生西瓜在西瓜育种中具有重要作用,然而目前对西瓜属物种间亲缘关系的研究十分有限,而且对西瓜属物种的分类问题还存在分歧.比较基因组原位杂交是分析物种间亲缘关系的有效手段,本研究以西瓜基因组DNA作探针,分别对缺须西瓜、热迷西瓜、药西瓜和诺丹西瓜有丝分裂中期染色体进行了比较基因组原位杂交分析,揭示了西瓜属物种间的亲缘关系,同时对分类地位尚存在争议的诺丹西瓜的归属问题进行了分析,发现诺丹西瓜和甜瓜之间具有非常近的亲缘关系,本研究结果为西瓜与近缘种间的远缘杂交提供了重要的理论依据.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F(8) population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ～800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.     

A CHLOROPLAST-DNA PHYLOGENY OF THE WILD PERENNIAL RELATIVES OF SOYBEAN (GLYCINE SUBGENUS GLYCINE): CONGRUENCE WITH MORPHOLOGICAL AND CROSSING GROUPS

Hypotheses of evolutionary relationships among the Australian wild perennial relatives of soybean (Glycine subgenus Glycine) are based largely on patterns of meiotic pairing in intra- and interspecific experimental hybrids. This evidence has indicated a number of genome groupings within the subgenus but has not resolved most phylogenetic relationships. Restriction-endonuclease site variation of chloroplast DNA (cpDNA) within the perennial subgenus is reported here, representing a sampling of approximately 3% of the approximately 150-kilobase plastome. Seven hundred twenty-one unique restriction sites were compared within Glycine using 29 restriction endonucleases; 157 sites varied within the genus. Distance and parsimony methods using these data yielded congruent results, recognizing the existence of three major groups within subgenus Glycine: the species-rich and geographically diverse A clade consisting of G. canescens and related taxa; the B clade, which includes the stoloniferous species; and the C group, containing two species with distinctive curved pods. These results are in general agreement with hypotheses based on genome analysis; inconsistencies involve the inclusion of genetically divergent taxa such as G. falcata in well-supported plastome clades comprised of otherwise interfertile species. Such findings are not unexpected if crossing barriers are considered to be unique features of such anomalous species, paralleling their often numerous morphological and cpDNA autapomorphies. Consideration of cpDNA divergence within the three major clades of subgenus Glycine indicates that the rate of plastome evolution is uncoupled from rates of morphological or ecological diversification.     

Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers

Low polymorphism in cultivated watermelon has been reported in previous studies, based mainly on US Plant Introductions and watermelon cultivars, most of which were linked to breeding programmes associated with disease resistance. Since germplasm sampled in a putative centre of origin in southern Africa may harbour considerably higher variability, DNA marker-based diversity was estimated among 81 seedlings from eight accessions of watermelon collected in Zimbabwe; five accessions of cow-melons (Citrullus lanatus var. citroides) and three of sweet watermelons (C. lanatus var. lanatus). Two molecular marker methods were used, random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) also known as microsatellite DNA. Ten RAPD primers produced 138 markers of which 122 were polymorphic. Nine SSR primer pairs detected a total of 43 alleles with an average of 4.8 alleles per locus. The polymorphic information content (PIC) ranged from 0.47 to 0.77 for the RAPD primers and from 0.39 to 0.97 for the SSR loci. Similarity matrices obtained with SSR and RAPD, respectively, were highly correlated but only RAPD was able to provide each sample with an individual-specific DNA profile. Dendrograms and multidimensional scaling (MDS) produced two major clusters; one with the five cow-melon accessions and the other with the three sweet watermelon accessions. One of the most variable cow-melon accessions took an intermediate position in the MDS analysis, indicating the occurrence of gene flow between the two subspecies. Analysis of molecular variation (AMOVA) attributed most of the variability to within-accessions, and contrary to previous reports, sweet watermelon accessions apparently contain diversity of the same magnitude as the cow-melons.     

Inheritance of egusi seed type in watermelon

An unusual seed mutant in watermelon (Citrullus lanatus var. lanatus) has seeds with a fleshy pericarp, commonly called egusi seeds. The origin of the phenotype is unknown, but it is widely cultivated in Nigeria for the high protein and carbohydrate content of the edible seeds. Egusi seeds have a thick, fleshy pericarp that appears during the second to third week of fruit development. We studied the inheritance of this phenotype in crosses of normal seeded Charleston Gray and Calhoun Gray with two plant introduction accessions, PI 490383w and PI 560006, having the egusi seed type. We found that the egusi seed type is controlled by a single recessive gene, and the symbol eg was assigned.     

Cross pathogenicity studies with isolates of Fusarium oxysporum from either cucumber or watermelon pathogenic to both crop species*

Isolates of Fusarium oxysporum from Abaco, the Bahamas, whether obtained from wilted plants of cucumber (Cucumis sativus) or watermelon (Citrullus lanatus), were pathogenic to cucumber, watermelon, and cantaloupe (Cucumis melo var. reticulatus). The West Indian gherkin (Cucumis anguria), pumpkin (Cucurbita pepo), and three cultivars of summer squash (C. pepo var. melopepo) were not susceptible. Strains of F. oxysporum from wilted cucumber or watermelon plants from Florida were highly pathogenic only to their original host species and are regarded as different formae speciales.     

Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA

The 14 species of Crambe L. sect. Dendrocrambe DC. (Brassicaceae) form a monophyletic group endemic to the Canary and Madeira archipelagos. Both parsimony and maximum likelihood analyses of sequence data from the two internal transcribed spacer regions of nuclear ribosomal DNA were used to estimate phylogenetic relationships within this section. These analyses support the monophyly of three major clades. No clade is restricted to a single island, and therefore it appears that inter-island colonization has been the main avenue for speciation in these two archipelagos. The two species endemic to Fuerteventura (C. sventenii) and Madeira (C. fruticosa) comprise a clade, providing the first evidence for a floristic link between the Eastern Canary Islands and the archipelago of Madeira. Both maximum likelihood and weighted parsimony analyses show that this clade is sister to the two other clades, although bootstrap support for this relationship is weak. Parsimony optimizations of ecological zones and island distribution suggest a colonization route from the low-altitude areas of the lowland scrub toward the high-elevation areas of the laurel and pine forests. In addition, Tenerife is likely the ancestral island for species endemic to the five westernmost islands of Gran Canaria, La Gomera, El Hierro, La Palma, and Tenerife.     

非洲西瓜野生资源的化学成分分析及亲缘关系探讨

对引自非洲博茨瓦纳的１６份西瓜野生资源的有关化学成分进行了分析,同时对它们与栽培西瓜的亲缘关系作了探讨。结果表明,这批西瓜资源的种子脂肪主要由４种脂肪酸组成,即棕榈酸,油酸和亚油酸,其中饱和脂肪酸约占２０％,不饱和脂肪酸约占８０％,两种不饱和脂肪酸含量呈高度负相关。     

Evidence for host-specific clades of tetraphyllidean tapeworms (Platyhelminthes: Eucestoda) revealed by analysis of 18S ssrDNA

Sequence data from the V4 and V7-V9 variable regions of the 18S small subunit ribosomal DNA (ssrDNA) gene were used to examine relationships among 26 tetraphyllidean and two lecanicephalidean taxa. Newly collected specimens of 21 of the tetraphyllidean species were used to generate ssrDNA sequences that were combined with sequences previously available, including those of two diphyllidean taxa used for outgroup rooting. The sequences were aligned by eye according to secondary structural motifs of the conserved core of the molecule. Of the 1520 sites in the alignment, 874 (58%) were excluded from analysis due to alignment gaps and lack of positional homology as inferred by manual inspection. Genetic variability of the ssrDNA gene regions compared was greater than would be expected, based on the present taxonomy of the ingroup species, and the genetic divergences among tetraphyllidean 'families' and genera were comparable to that among tapeworm orders. Phylogenetic hypotheses were generated by the methods of maximum parsimony and maximum likelihood (GTR + I + Gamma nucleotide substitution model). Four most parsimonious trees resulted from analysis by maximum parsimony. Strict consensus of the four trees supported the monophyly of the Tetraphyllidea, with the lecanicephalidean taxa forming a sister lineage. Among the tetraphyllidean taxa included in the analysis were three major clades: a basal clade including species of the phyllobothriid genera Anthocephalum, Echeneibothrium, Rhinebothrium, Rhodobothrium and Spongiobothrium; a clade uniting the phyllobothriids of the genus Duplicibothrium with the dioecotaeniid genus Dioecotaenia; and a larger sister clade to the Duplicibothrium + Dioecotaenia clade that included the phyllobothriid genera Caulohothrium, Ceratobothrium, Clistobothrium, Paraoryigmatobothrium and Prosobothrium, the litobothriid genus Litobothrium and the onchobothriid genera Acanthobothrium, Calliobothrium, Phoreiobothrium and Platybothrium. Maximum likelihood analysis resulted in a topology that was congruent where nodes were strongly supported by parsimony analysis, but differed in the relative positions of the well-supported clades. In addition,maximum likelihood analysis grouped the lecanicephalidean taxa among the tetraphyllidean taxa, indicating paraphyly of the order Tetraphyllidea as currently defined. Relationships suggested by both methods of analysis reflected common host associations of the taxa better than their current classification, suggesting that coevolution has had a significant role in the evolution of the group.     

基于COⅠ和Cyt b基因序列的凤蝶科六属分子系统学研究

对凤蝶科6属25种的COⅠ基因和20种Cyt b基因的部分序列进行测定和分析, 探讨它们之间的系统发育关系; 以茶小卷叶蛾Adoxophyes honmai为外群, 用邻接法(neighbor-joining, NJ)、 最大简约法(maximum parsimony, MP)和贝叶斯法(Bayesian inference, BI)重建了凤蝶科6属的分子系统树。结果表明： COⅠ基因部分序列长度为661 bp, 其中保守位点417个, 可变位点244个, 简约信息位点191个; A+T的平均含量为70.3%, 明显高于C+G的平均含量29.6%。Cyt b基因部分序列长度为433 bp, 其中保守位点239个, 可变位点194个, 简约信息位点135个; A+T的平均含量为74.2%, 明显高于C+G的平均含量25.7%。分子系统树表明, 凤蝶属Papilio、 斑凤蝶属Chilasa、 尾凤蝶属Bhutanitis、 珠凤蝶属Pachliopta和喙凤蝶属Teinopalpus为单系性, 与传统形态分类结果相一致。但青凤蝶属Graphium单系性不够明确, 需要进一步探讨。研究结果为我国凤蝶科分子系统学研究积累了资料。     

The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.     

基于核基因c-mos的鸫亚科部分鸟类系统发生关系

采用分子系统学方法对鸫亚科Turdinae 11属21种鸟类的核基因c-mos进行了系统发生分析.所测序列经对位排列后共572个位点,其中核苷酸变异位点111个,简约信息位点71个.以太平鸟Bombycilla garrulus作外群,采用邻接法、最大简约法和最大似然法分别构建其系统发生树.重建的系统发生树显示:所研究鸫亚科21种鸟类分成2个支系,第1个支系包括鸫属Turdus和地鸫属Zoothera.第2个支系包括红尾鸲属Phoenicurus、矶鸫属Monticola、水鸲属Rhyacornis、鸲属Tarsiger、溪鸲属Chainarrornis、石即鸟属Saxicola、燕尾属Enivurus、歌鸲属Luscinia和鹊鸲属Copsychus.红尾鸲属为并系类群,水鸲属和溪鸲属聚到这一支系;歌鸲属与燕尾属互为姐妹群,再与鸲属聚合构成另一支系;宝兴歌鸫Turdus mupinensis独立于鸫属及地鸫属之外,形成单独一个分支.     

枇杷属内栽培种和部分野生种ITS序列分析

对不同栽培区的25种普通枇杷品种以及7种枇杷属野生种的ITS序列进行扩增并测序,采用邻接法和最大简约法进行系统发育树的构建并对枇杷属内不同种间的遗传关系进行了分析。结果表明:枇杷属植物ITS序列ITS1+5.8S rDNA+ITS2总长度为592 bp或594 bp,长度变化发生在ITS2。所有样本的ITS1和5.8S rDNA长度一样,都是223 bp和168 bp;而ITS2为201 bp或203 bp。5种枇杷属野生种的ITS序列长度为594 bp,包括栎叶枇杷、大渡河枇杷、南亚枇杷、南亚枇杷窄叶变种和大瑶山枇杷;其余2种枇杷属野生种(麻栗坡枇杷、小叶枇杷)和普通枇杷栽培种的ITS序列长度都为592 bp。所有样本ITS序列的GC含量为64.2%~64.5%,其中ITS1为64.1%~65.5%,ITS2为68.1%~72.6%。对所有样本的ITS序列比对产生44个可变位点,其中38个为简约信息位点,其中11个位于ITS1,5个位于5.8S rDNA,22个位于ITS2。最大的种间序列差异为7.7%,最小的种间差异发生在麻栗坡枇杷和小叶枇杷之间,仅为0.2%。普通枇杷种内的ITS序列差异很低,25种普通枇杷栽培种之间的序列差异为0~1.5%。所研究的枇杷属植物可分为3个分支。分支Ⅰ包括所有普通枇杷品种,分支Ⅱ包含5种野生枇杷种,包括栎叶枇杷、大渡河枇杷、南亚枇杷、南亚枇杷窄叶变种和大瑶山枇杷;分支Ⅲ由2个野生枇杷种(麻栗坡枇杷、小叶枇杷)组成。该研究结果表明ITS序列对枇杷种间鉴定和系统发育分析具有一定意义,但对普通枇杷栽培种间的鉴定作用不大。     

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

? Premise of the study: The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. ? Methods: The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. ? Key results: Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. ? Conclusions: Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.     

Molecular systematics of a speciose, cosmopolitan songbird genus: defining the limits of, and relationships among, the Turdus thrushes

The avian genus Turdus is one of the most speciose and widespread of passerine genera. We investigated phylogenetic relationships within this genus using mitochondrial DNA sequence data from the ND3, ND2 and cytochrome b genes. Our sampling of Turdus included 60 of the 65 extant species currently recognized, as well as all four species from three genera previously shown to fall inside Turdus (Platycichla, Nesocichla, and Cichlherminia). Phylogenetic trees based on maximum likelihood and maximum parsimony algorithms were congruent. Most of the Turdus taxa sampled fall into one of four clades: an African clade, a Central American-Caribbean clade, a largely South American clade, and a Eurasian clade. Still other taxa are placed either at the base of Turdus, or as links between clades. In no instance is any continent reciprocally monophyletic for the species distributed on it. A general lack of nodal support near the base of the phylogeny seems related to a rapid intercontinental establishment of the major clades within Turdus very early in the history of the genus. The monotypic genus Psophocichla is distantly related to, but clearly the sister of, Turdus rather than a constituent member of it.     

The molecular phylogeny of Rebutia (Cactaceae) and its allies demonstrates the influence of paleogeography on the evolution of South American mountain cacti

The tropical Andes harbor a major part of the world's plant biodiversity. The montane cacti of the tribes Browningieae, Cereeae, and Trichocereeae underwent extensive radiation and thus are well suited as a model group to study the diversification of Andean plants. We reconstructed their phylogeny employing three noncoding chloroplast regions and explained it in the context of the geological history of South America. We found that the clade of cephalia-bearing cacti with naked pericarpels is centered in northeastern Brazil, whereas almost all other clades comprise Andean species. The spatial split between the clades was probably caused by the Andean uplift and the concurrent formation of intracontinental marine basins in the Tertiary. The phylogenetic reconstructions based on parsimony and Bayesian approaches do not reflect the traditional delimitation of the tribes and of the large genera. Our results suggest that Rebutia s.l. and Echinopsis s.l. are not monophyletic and that Sulcorebutia, Weingartia, and Cintia should be united into one genus. Even though this "Weingartia-complex" and the genus Gymnocalycium are similar in size and morphological diversity, Gymnocalycium has a very high molecular divergence suggesting a comparably older radiation.     

A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology

Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF-rpl32, rpl32-trnL, and psbM-psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS-derived and cpDNA-derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.     

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca ), some Australian species of Melaleuca , a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea , and Regelia , and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus , and Phymatocarpus . All molecular analyses sup port the monophyly of Conothamnus and of Regelia , genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia . The findings have implications for both taxonomy and biogeography.