Comparative analysis of rice MADS-box genes expressed during flower development

MADS-box genes involved in flower development have been isolated and studied in a wide variety of plant species. However, most of these studies are related to dicot species like Antirrhinum majus, Arabidopsis thaliana and Petunia hybrida. Although the floral structures of typical monocot and dicot flowers differ substantially, previous studies indicate that MADS-box genes controlling floral organ identity in dicots can also be identified in monocot plants like rice and maize. To extend this study further to obtain a more global picture of monocot and dicot MADS-box gene evolution, we performed a phylogenetic study using MADS-box genes from A. thaliana and Oryza sativa. Furthermore, we investigated whether the identified orthologues of Arabidopsis and rice have a conserved expression profile that could indicate conservation of function.     

甘蓝型油菜MADS-box基因家族的鉴定与系统进化分析

MADS-box基因家族参与调控开花时间、花器官分化、根系生长、分生组织分化、子房和配子发育、果实膨大及衰老等植物生长发育的重要过程。基于甘蓝型油菜(Brassica napus)基因组测序数据,利用生物信息学方法对甘蓝型油菜MADS-box基因家族进行鉴定和注释及基因结构与系统进化分析。结果显示,在甘蓝型油菜中鉴定出307个MADS-box基因家族成员,根据进化关系可将其分为两大类型,I型(M-type)包含α、β、γ三个亚家族,II型(MIKC-type)包括MIKCC和MIKC*两个亚家族,MIKCC可进一步分为13个小类;甘蓝型油菜A基因组染色体上分布的MADS-box基因多于C基因组。在基因结构上,MIKC-type亚家族基因序列普遍比M-type长且含有较多的外显子;M-type亚家族蛋白序列中的motif数量为2–5个,MIKC-type亚家族蛋白序列中平均含有7个motif。拟南芥(Arabidopsis thaliana)与甘蓝型油菜MADS-box基因共线性分析结果显示,全基因组复制事件对MADS-box基因家族尤其是MIKC亚家族的扩张起重要作用;MIKC亚家族基因在进化过程中受到的选择压力约为M-type的2倍,这表明MIKC-type亚家族在进化过程中被选择性保留。     

苹果DREB转录因子家族全基因组鉴定与分析

DREB转录因子属于AP2/ERF转录因子家族,能够与DRE/CRT顺式作用元件特异性结合,调控与逆境应答基因的表达,因而在植物应对低温、干旱、高盐等逆境胁迫中发挥重要作用。该研究利用苹果全基因组数据,通过生物信息学手段鉴定苹果DREB转录因子家族成员,并分析DREB转录因子家族保守域特点与功能及表达情况。结果表明:从苹果全基因组中共鉴定出60个DREB转录因子家族成员,与拟南芥和水稻相比基本一致,通过引入拟南芥DREB基因进行系统发生分析,进一步可以将其细分为6个亚组;结构域和保守元件分析表明,DREB基因家族含有一个AP2保守结构域;染色体定位表明,苹果DREB基因分布于11条染色体上,部分基因存在串联复制现象;基因结构分析显示,该亚家族基因不含内含子。利用同源拟南芥RNA-Seq数据分析结果表明,DREB转录因子家族对低温、ABA调节等非生物胁迫具有调控作用,同时在DREB亚家族中每个亚组响应不同的非生物胁迫;通过分析DREB基因在不同组织中的表达情况,结果显示DREB基因在植物根部中的表达量最强,其次是叶。     

In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants

In the sequences released by the Arabidopsis Genome Initiative (AGI), we discovered a new and unexpectedly large family of orphan genes (127 genes by 01.08.99), named AtPCMP. The distribution of the AtPCMP genes on the five chromosomes suggests that the genome of Arabidopsis thaliana contains more than 200 genes of this family (1% of the whole genome). The deduced AtPCMP proteins are characterized by a surprising combinatorial organization of sequence motifs. The amino-terminal domain is made of a succession of three conserved motifs which generate an important diversity. These proteins are classified into three subfamilies based on the length and nature of their carboxy-terminal domain constituted by 1–6 motifs. All the motifs characterized have an important level of conservation in both sequence and spacing. A specific signature of this large family is defined. The presence of ESTs in databases and the detection of clones in A. thaliana cDNA libraries indicate that most of the genes of this family are expressed. The absence of similar sequences outside the plant kingdom strongly suggests that this unusually large orphan family is unique to plants. Features, the genesis, the potential function and the evolution of this plant combinatorial and modular protein family are discussed.     

萝卜TALE转录因子家族的鉴定与分析

TALE (three-amino acid loop extension)转录因子在植物生长发育及细胞分化过程中起重要作用.在多种植物中均已鉴定出TALE转录因子的家族成员,但是萝卜TALE转录因子家族的研究鲜有报道.文中通过生物信息学手段在象牙白萝卜全基因组中鉴定出了分布于9条染色体上的33个TALE家族基因.研究...     

Motifs specific for the ADR1 NBS–LRR protein family in <Emphasis Type="Italic">Arabidopsis</Emphasis> are conserved among NBS–LRR sequences from both dicotyledonous and monocotyledonous plants

The activated disease resistance (ADR) 1 gene encodes a protein that possesses an N-terminal coiled-coil (CC) motif, nucleotide-binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. ADR1 belongs to a small, atypical Arabidopsis thaliana sub-class containing four CC–NBS–LRR genes. The NBS region of most NBS–LRR proteins possesses numerous conserved motifs. In contrast, the LRR domain, which is subject to positive selection, is highly variable. Surprisingly, sequence analysis revealed that the LRR domain of the ADR1 sub-class was more conserved than the NBS region. Sequence analysis identified two novel conserved motifs, termed TVS and PKAE, specific for this CC–NBS–LRR sub-class. The TVS motif is adjacent to the P-loop, whereas the PKAE motif corresponded to the inter-domain region termed the NBS–LRR linker, which was conserved within the different CC–NBS–LRR classes but varied among classes. These ADR1-specific motifs were employed to identify putative ADR1 homologs in phylogenetically distant and agronomically important plant species. Putative ADR1 homologs were identified in 11 species including rice and in 3 further Poaceae species. The ADR1 sub-class of CC–NBS–LRR proteins is therefore conserved in both monocotyledonous and dicotyledonous plant species.     

Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation

There are two groups of MADS intervening keratin-like and C-terminal (MIKC)-type MADS box genes, MIKC^C type and MIKC* type. In seed plants, the MIKC^C type shows considerable diversity, but the MIKC* type has only two subgroups, P- and S-clade, which show conserved expression in the gametophyte. To examine the functional conservation of MIKC*-type genes, we characterized all three rice (Oryza sativa) MIKC*-type genes. All three genes are specifically expressed late in pollen development. The single knockdown or knockout lines, respectively, of the S-clade MADS62 and MADS63 did not show a mutant phenotype, but lines in which both S-clade genes were affected showed severe defects in pollen maturation and germination, as did knockdown lines of MADS68, the only P-clade gene in rice. The rice MIKC*-type proteins form strong heterodimeric complexes solely with partners from the other subclade; these complexes specifically bind to N10-type C-A-rich-G-boxes in vitro and regulate downstream gene expression by binding to N10-type promoter motifs. The rice MIKC* genes have a much lower degree of functional redundancy than the Arabidopsis thaliana MIKC* genes. Nevertheless, our data indicate that the function of heterodimeric MIKC*-type protein complexes in pollen development has been conserved since the divergence of monocots and eudicots, roughly 150 million years ago.