Determination of Flower Structure in Elaeis guineensis: Do Palms use the Same Homeotic Genes as Other Species?

AIMS: In this article a review is made of data recently obtained on the structural diversity and possible functions of MADS box genes in the determination of flower structure in the African oil palm (Elaeis guineensis). MADS box genes play a dominant role in the ABC model established to explain how floral organ identity is determined in model dicotyledon species such as Arabidopsis thaliana and Antirrhinum majus. In the monocotyledons, although there appears to be a broad general conservation of ABC gene functions, the model itself needs to be adapted in some cases, notably for certain species which produce flowers with sepals and petals of similar appearance. For the moment, ABC genes remain unstudied in a number of key monocot clades, so only a partial picture is available for the Liliopsida as a whole. The aim of this article is to summarize data recently obtained for the African oil palm Elaeis guineensis, a member of the family Arecaceae (Arecales), and to discuss their significance with respect to knowledge gained from other Angiosperm groups, particularly within the monocotyledons. SCOPE: The essential details of reproductive development in oil palm are discussed and an overview is provided of the structural and functional characterization of MADS box genes likely to play a homeotic role in flower development in this species. CONCLUSIONS: The structural and functional data provide evidence for a general conservation of the generic 'ABC' model in oil palm, rather than the 'modified ABC model' proposed for some other monocot species which produce homochlamydeous flowers (i.e. with morphologically similar organs in both perianth whorls), such as members of the Liliales. Our oil palm data therefore follow a similar pattern to those obtained for other Commelinid species in the orders Commelinales and Poales. The significance of these findings is discussed.     

Characterization of oil palm MADS box genes in relation to the mantled flower abnormality

In vitro propagation of oil palm (Elaeis guineensis Jacq.) frequently induces a somaclonal variant called ‘mantled’ abnormality, in which the stamens of both male and female flowers are transformed into carpels. This leads to a reduced yield or complete loss of the harvest of palm oil. The high frequency of the abnormality in independent lines and the high reversal rate suggest that it is due to an epigenetic change. The type of morphological changes suggest that it involves homeotic MADS box genes that regulate the identity of the flower whorls. We have isolated a number of MADS box genes from oil palm inflorescences by a MADS box-directed mRNA display approach. The isolated partial cDNAs included genes that were likely to function at the initial stages of flowering as well as genes that may function in determination of the inflorescence and the identity of the flower whorls. For four genes that were homologous to genes known to affect the reproductive parts of the flower, full length cDNAs were isolated. These were a B-type MADS box gene which may function in the determination of stamen formation, a C-type gene expected to be involved in stamen and carpel formation, and two putative SEP genes which act in concert with the A-, B- and C-type MADS box gene in determining flower whorl formation. The B-type gene EgMADS16 was functionally characterized as a PISTILLATA orthologue; it was able to complement an Arabidopsis thaliana pi mutant. Whether EgMADS16, or any of the other EgMADS genes, are functionally involved in the mantled condition remains to be established.     

基于RNA-seq对南蛇藤MADS-box转录因子序列及表达分析

为了分析南蛇藤MADS-box转录因子对其雌花发育和果实形成的调控信息,本文基于南蛇藤的转录组数据,获得15个具有全长开放阅读框的MADS-box转录因子（ColMADS）,并利用生物信息学方法对其性质和结构特性进行了分析。结果表明,基因comp37814_g1和comp41380_g2属于M-type家族,不含有K盒结构,其他均为MIKC家族;除了comp37713_g1之外,其余均属于不稳定的亲水性蛋白;二级结构均含有α-螺旋、扩展链结构、β-转角和无规则卷曲,其中α-螺旋所占比例最高;序列主要包含5种保守基序,基序1和基序2分别含50个氨基酸且属于该基因家族的保守基序,仅基序1含有MADS盒。系统进化分析结果显示南蛇藤ColMADS转录因子被分为10个进化支,分属于不同类型的亚家族及不同的组。另外,利用荧光定量PCR检测方法揭示了这些基因在南蛇藤盛花、落花和幼果不同发育时期的表达情况。结果表明,2个基因在盛花期相对表达值最高,9个基因在落花期相对表达值最高,在幼果形成过程中有4个基因显著上调表达。     

Functional characterization of MADS box genes involved in the determination of oil palm flower structure

In order to study the molecular regulation of flower development in the monoecious species oil palm (Elaeis guineensis), cDNAs of 12 MADS box genes from this plant belonging to seven distinct subfamilies were previously isolated and characterized. Here studies carried out on five of these genes, each likely to be involved in floral morphogenesis: EgSQUA1 (SQUAMOSA subfamily); EgAGL2-1 (AGL2 subfamily); EgGLO2 (GLOBOSA subfamily); EgDEF1 (DEFICIENS subfamily); and EgAG2 (AGAMOUS subfamily), are described. In order to determine where and when in the plant these genes are likely to function, their spatial and temporal patterns of expression were studied during the development of male and female inflorescences, either of normal phenotype or displaying a homeotic flowering abnormality known as mantled. In parallel, the phenotypic effects of ectopically expressing these genes in transgenic Arabidopsis thaliana plants were analysed. The data suggest a broad conservation of floral homeotic gene functions between oil palm and previously described model species, although a few minor variations in the zones of activity of certain genes cannot be excluded. The data also indicate distinct molecular identities for the morphologically similar floral organs of whorls 1 and 2. They also reveal reduced expression of putative B, C/D, and E class genes in mantled flowers, which undergo a homeotic transformation comparable to B class mutants of model species.     

风信子HoMADS2基因的克隆及表达分析

利用同源克隆策略,从风信子中分离出一个MADS box基因,命名为HoMADS2。序列比较分析表明,HoMADS2与B类MADS box蛋白具有较高的同源性。分子进化树分析显示,HoMADS2与PI家族类聚在一起。同时,在HoMADS2的Kbox和C末端区域均具有PI家族的特征序列。以上序列分析结果表明,HOMADS2可能是尸,的一个同源基因。RNA分子杂交结果显示,HoMADS2在四轮花器官中均表达,其表达模式不同于双子叶植物中尸,同源基因。利用风信子离体花器官再生系统研究表明,HoMADS2在再生花芽中的表达不同于HoMADS1和HAG1,该基因在再生花芽发育过程中组成型表达,不受外源细胞分裂素和生长素的影响。     

Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon

The avian family Accipitridae has historically been divided into subfamilies or tribes based on features such as general resemblance, feeding ecology, and behavior. Consequently, the monophyly of those groups has been questionable. Recently, three phylogenetic analyses of a majority of the genera have appeared, one based on osteology, one on DNA sequences from a single mitochondrial gene, and the third on mitochondrial plus nuclear DNA sequences, and the resulting phylogenies were in substantial disagreement concerning the composition and basal branching patterns of the clades and hence require further analysis and confirmation. Here we use DNA sequences from the large nuclear RAG-1 exon to investigate the phylogenetic relationships of these birds. Our results largely corroborated the prior study that included nuclear genes. We found strong support for a monophyletic clade comprising the secretarybird Sagittarius serpentarius , the osprey Pandion haliaetus , and the traditional accipitrids. However, every one of the traditionally recognized subfamilies of accipitrids was found to be polyphyletic. The most basal nodes in the phylogeny separate small clades of insectivorous and scavenger species, such as kites and Old World vultures, from the rest of the family. The speciose genera of bird and mammal predators are all relatively derived (terminal) in the phylogeny. Many of the basal clades are cosmopolitan in their distributions, consistent with the great mobility of these raptors. A new classification is proposed that eliminates the problem of polyphyletic intrafamilial taxa.     

Phylogenetic utility of the nuclear gene malate synthase in the palm family (Arecaceae)

There is currently a shortage of DNA regions known to be useful for phylogenetic research in palms (Arecaceae). We report the development and use of primers for amplifying and sequencing regions of the nuclear gene malate synthase. In palms the gene appears to be single-copy, with exon regions that are phylogenetically informative within the family. We constructed a phylogeny of 45 palms and five outgroup taxa using 428 bp of malate synthase exon regions. We found that some major clades within the family were recovered, but there was a lack of resolution among the genera in subfamilies Arecoideae, Ceroxyloideae, Coryphoideae, and Phytelephantoideae. In a second analysis, malate synthase exon regions totaling 1002 bp were sequenced for 16 palms and two outgroup taxa. There was increased bootstrap support for some groups and for the placement of the monotypic genus Nypa as sister to the rest of the family. A comparison with data sets from noncoding regions of the chloroplast genome indicates that malate synthase sequences are more variable and potentially contain more phylogenetic information. We found no evidence of multiple copies of the malate synthase gene in palm genomes.     

Diverse roles for MADS box genes in Arabidopsis development.

Members of the MADS box gene family play important roles in flower development from the early step of determining the identity of floral meristems to specifying the identity of floral organ primordia later in flower development. We describe here the isolation and characterization of six additional members of this family, increasing the number of reported Arabidopsis MADS box genes to 17. All 11 members reported prior to this study are expressed in flowers, and the majority of them are floral specific. RNA expression analyses of the six genes reported here indicate that two genes, AGL11 and AGL13 (AGL for AGAMOUS-like), are preferentially expressed in ovules, but each has a distinct expression pattern. AGL15 is preferentially expressed in embryos, with its onset at or before the octant stage early in embryo development. AGL12, AGL14, and AGL17 are all preferentially expressed in root tissues and therefore represent the only characterized MADS box genes expressed in roots. Phylogenetic analyses showed that the two genes expressed in ovules are closely related to previously isolated MADS box genes, whereas the four genes showing nonfloral expression are more distantly related. Data from this and previous studies indicate that in addition to their proven role in flower development, MADS box genes are likely to play roles in many other aspects of plant development.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Functional analysis of three lily (Lilium longiflorum) APETALA1-like MADS box genes in regulating floral transition and formation

Three cDNAs showing a high degree of homology to the SQUA subfamily of MADS box genes were isolated and characterized from the lily (Lilium longiflorum). Lily MADS Box Gene 5 (LMADS5) showed high sequence identity to oil palm (Elaeis guineensis) SQUAMOSA3 (EgSQUA3). LMADS6 is closely related to LMADS5 whereas LMADS7 is more related to DOMADS2, an orchid (Dendrobium) gene in the SQUA subfamily. The expression pattern for these three genes was similar and their RNAs were detected in vegetative stem and inflorescence meristem. LMADS5 and 6 were highly expressed in vegetative leaves and carpel, whereas LMADS7 expression was absent. Ectopic expression of LMADS5, 6 or 7 in transgenic Arabidopsis plants showed novel phenotypes by flowering early and producing terminal flowers. Homeotic conversions of sepals to carpelloid structures and of petal to stamen-like structures were also observed in 35S::LMADS5, 6 or 7 flowers. Ectopic expression of LMADS6 or LMADS7 was able to complement the ap1 flower defect in transgenic Arabidopsis ap1 mutant plants. These results strongly indicated that the function of these three lily genes was involved in flower formation as well as in floral induction. Furthermore, the ability of lily LMADS6 and 7 to complement the Arabidopsis ap1 mutant provided further evidence to show that the conserved motifs (paleoAP1 or euAP1) in the C-terminus of the SQUA/AP1 subfamily of MADS box genes is not strictly necessary for their function.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

墨兰多舌奇花MADS特异表达基因筛选及分析

以墨兰‘南菊’为代表,用抑制消减杂交和基因芯片相结合技术构建墨兰多舌与正格花舌间的差异表达基因文库,筛选与花形态建成相关的MADS差异表达基因并构建系统进化树。结果表明:在多舌瓣中筛选出32个上调表达MADS基因,包括TM6、AG、AP1、DEF1、AP3及PI基因。其中有10个基因与AGL17、AGL29、FUI聚为一类,12个基因与其他的MADS基因归为一类。这些MADS基因参与了多舌瓣发生,并可能扮演了重要角色。该研究可为从兰花多舌变化的角度阐明墨兰奇花形成的分子机理及培育中国兰花新奇优良品种提供思路和理论依据。     

Phylogeny and genomic organization of the TIR and non-tIR NBS-LRR resistance gene family in Medicago truncatula

Sequences homologous to the nucleotide binding site (NBS) domain of NBS-leucine-rich repeat (LRR) resistance genes were retrieved from the model legume M. truncatula through several methods. Phylogenetic analysis classified these sequences into TIR (toll and interleukin-1 receptor) and non-TIR NBS subfamilies and further subclassified them into several well-defined clades within each subfamily. Comparison of M. truncatula NBS sequences with those from several closely related legumes, including members of the tribes Trifoleae, Viceae, and Phaseoleae, reveals that most clades contain sequences from multiple legume species. Moreover, sequences from species within the closely related Trifoleae and Viceae tribes (e.g., Medicago and Pisum spp.) tended to be cophyletic and distinct from sequences of Phaseoleae species (e.g., soybean and bean). These results suggest that the origin of major clades within the NBS-LRR family predate radiation of these Papilionoid legumes, while continued diversification of these sequences mirrors speciation within this legume subfamily. Detailed genetic and physical mapping of both TIR and non-TIR NBS sequences in M. truncatula reveals that most NBS sequences are organized into clusters, and few, if any, clusters contain both TIR and non-TIR sequences. Examples were found, however, of physical clusters that contain sequences from distinct phylogenetic clades within the TIR or non-TIR subfamilies. Comparative mapping reveals several blocks of resistance gene loci that are syntenic between M. truncatula and soybean and between M. truncatula and pea.     

Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.)

Oil palm (Elaeis guineensis Jacq.) is an economically important crop, which is grown for oil production. To better understand the molecular basis of oil palm chloroplasts, we characterized the complete chloroplast (cp) genome sequence obtained from 454 pyrosequencing. The oil palm cp genome is 156,973 bp in length consisting of a large single-copy region of?85,192 bp flanked on each side by inverted repeats of 27,071 bp with a small single-copy region of 17,639 bp joining the?repeats. The genome contains 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. By aligning the cp?genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes. Creation of an initiation codon by RNA editing in rpl2 has been reported in several monocots and was also found in the oil palm cp genome. Fifty common chloroplast protein-coding genes from 33 plant taxa were used to construct ML and MP?phylogenetic trees. Their topologies are similar and strongly support for the position of E. guineensis as the sister of closely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.