Long non-coding RNAs(lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. I...Long non-coding RNAs(lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position.Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants.展开更多
RAB guanosine triphosphatases （GTPases） are key regulators of vesicle trafficking and are essential to the growth and development of all eukaryotic cells. During evolution, the RAB family has expanded in different p...RAB guanosine triphosphatases （GTPases） are key regulators of vesicle trafficking and are essential to the growth and development of all eukaryotic cells. During evolution, the RAB family has expanded in different patterns to facilitate distinct cellular, developmental and physiological adaptations. Yeast has only 11 family members, whereas mammalian RABs have expanded to 18 RAB subfamilies. Plant RABs have diversified primarily by duplicating members within a single subfamily. Plant RABs are divided into eight subfamilies, corresponding to mammalian RAB1, RAB2, RAB5, RAB6, RAB7, RAB8, RAB11 and RAB18. Functional diversification of these is exemplified by the RAB1 ls, orthologs of which are partitioned into unique cell compartments in plants where they function to transport vesicles during localized tip growth. Similarly, the RAB2 family in grasses is likely involved in vesicle secretion associated with wall expansion, as determined by analysis of over-expression mutants. We propose that dicots and monocots have also diverged in their RAB profiles to accommodate unique cellular functions between the two groups. Here we present a bioinformatics analysis comparing the RAB sub-families of rice, maize and Arabidopsis. These results will guide future functional studies to test for the role of diversification of subfamilies unique to monocots compared to dicots.展开更多
Doubled haploid(DH) technology is used to obtain homozygous lines in a single generation, a technique that significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DH...Doubled haploid(DH) technology is used to obtain homozygous lines in a single generation, a technique that significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but this technique is limited by species and genotype recalcitrance. In vivo haploid induction(HI) through seed is widely and efficiently used in maize and was recently extended to several other crops. Here we show that in vivo HI can be triggered by mutation of DMP maternal haploid inducer genes in allopolyploid(allotetraploid) Brassica napus and Nicotiana tabacum. We developed a pipeline for selection of DMP orthologs for clustered regularly interspaced palindromic repeats mutagenesis and demonstrated average amphihaploid induction rates of2.4% and 1.2% in multiple B. napus and N. tabacum genotypes, respectively. These results further confirmed the HI ability of DMP gene in polyploid dicot crops. The DMP-HI system offers a novel DH technology to facilitate breeding in these crops. The success of this approach and the conservation of DMP genes in dicots suggest the broad applicability of this technique in other dicot crops.展开更多
Coriaria,the only genus under family Coriariacea,receives a lot interest among botanist due to its controversial taxonomic treatment and unique phytochemistry that could be commercially important.The populations of Co...Coriaria,the only genus under family Coriariacea,receives a lot interest among botanist due to its controversial taxonomic treatment and unique phytochemistry that could be commercially important.The populations of Coriaria japonica subsp.intermedia in Cordillera Central Range(CCR),Philippines had never been studied in detail.With the need for more information on this controversial genus,the study deemed it necessary to present the distribution and morpho-anatomical description of C.japonica subsp.intermedia in CCR.A total of 123 populations were documented,found at an elevation range of 1334 to 2494 m asl and stretched between16°31’37.7"to 17°5’47.8"N and 120°39’40.3"to120°55’48"E.Mapping these populations showed a narrow linear pattern of distribution concentrated at the southern portion of CCR.The plant is a shrub with simple leaves,collateral buds,raceme inflorescence,bisexual flowers with persistent perianth forming an accessory fruit after fertilization.In terms of anatomy,much are of the usual dicot characters such as dorsiventral leaf with stomata concentrated in the lower epidermis,eustele with pith in the stem andpresence of secondary growth both on old stem and old root.Interesting findings of the study include the123 populations,the larger leaf measurements,longer petals and larger fruits than the original description given by Matsumura.Also,the paracytic type of stomata and presence of pith in the primary roots of C.japonica subsp.intermedia are interesting since these are common monocot characters while the plant is dicot.These findings are additional information that could help clear the controversies on the genus Coriaria.More importantly,our results could provide essential information for understanding the plant and for developing conservation strategies not just for this plant but also for the other related plants in the CCR biogeographical zone.展开更多
An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot dive...An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.展开更多
基金supported by Zhejiang Provincial Natural Science Foundation of China (LR16C060001)the National Key Program on Transgenic Researchthe Fundamental Research Funds for the Central Universities (2016QNA6014)
文摘Long non-coding RNAs(lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position.Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants.
基金Supported by the National Natural Science Foundation of China(30260062)to Jiaming Zhangthe US Department of Energy,Division of Energy Biosciences(PR 03-00ER15098.00)+1 种基金US Department of Agriculture-NRI(2001-35304-09899)National Science Foundation-Plant Genome Research Program DBI#0501862 to Anne Sylvester.
文摘RAB guanosine triphosphatases （GTPases） are key regulators of vesicle trafficking and are essential to the growth and development of all eukaryotic cells. During evolution, the RAB family has expanded in different patterns to facilitate distinct cellular, developmental and physiological adaptations. Yeast has only 11 family members, whereas mammalian RABs have expanded to 18 RAB subfamilies. Plant RABs have diversified primarily by duplicating members within a single subfamily. Plant RABs are divided into eight subfamilies, corresponding to mammalian RAB1, RAB2, RAB5, RAB6, RAB7, RAB8, RAB11 and RAB18. Functional diversification of these is exemplified by the RAB1 ls, orthologs of which are partitioned into unique cell compartments in plants where they function to transport vesicles during localized tip growth. Similarly, the RAB2 family in grasses is likely involved in vesicle secretion associated with wall expansion, as determined by analysis of over-expression mutants. We propose that dicots and monocots have also diverged in their RAB profiles to accommodate unique cellular functions between the two groups. Here we present a bioinformatics analysis comparing the RAB sub-families of rice, maize and Arabidopsis. These results will guide future functional studies to test for the role of diversification of subfamilies unique to monocots compared to dicots.
基金supported by National Key Research and Development Program of China (2016YFD0101200, 2018YFD0100201)China Agriculture Research System of MOF and MARA, National Natural Science Foundation of China (91935303, 32001554)+1 种基金the 2020 Research Program of Sanya Yazhou Bay Science and Technology City (SKJC-2020-02-003)China Postdoctoral Science Foundation (2020TQ0356)
文摘Doubled haploid(DH) technology is used to obtain homozygous lines in a single generation, a technique that significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but this technique is limited by species and genotype recalcitrance. In vivo haploid induction(HI) through seed is widely and efficiently used in maize and was recently extended to several other crops. Here we show that in vivo HI can be triggered by mutation of DMP maternal haploid inducer genes in allopolyploid(allotetraploid) Brassica napus and Nicotiana tabacum. We developed a pipeline for selection of DMP orthologs for clustered regularly interspaced palindromic repeats mutagenesis and demonstrated average amphihaploid induction rates of2.4% and 1.2% in multiple B. napus and N. tabacum genotypes, respectively. These results further confirmed the HI ability of DMP gene in polyploid dicot crops. The DMP-HI system offers a novel DH technology to facilitate breeding in these crops. The success of this approach and the conservation of DMP genes in dicots suggest the broad applicability of this technique in other dicot crops.
基金financial support provided by Benguet State University though the Office of the Vice-President for Research and Extension headed by Dr.Carlito P.Laurean。
文摘Coriaria,the only genus under family Coriariacea,receives a lot interest among botanist due to its controversial taxonomic treatment and unique phytochemistry that could be commercially important.The populations of Coriaria japonica subsp.intermedia in Cordillera Central Range(CCR),Philippines had never been studied in detail.With the need for more information on this controversial genus,the study deemed it necessary to present the distribution and morpho-anatomical description of C.japonica subsp.intermedia in CCR.A total of 123 populations were documented,found at an elevation range of 1334 to 2494 m asl and stretched between16°31’37.7"to 17°5’47.8"N and 120°39’40.3"to120°55’48"E.Mapping these populations showed a narrow linear pattern of distribution concentrated at the southern portion of CCR.The plant is a shrub with simple leaves,collateral buds,raceme inflorescence,bisexual flowers with persistent perianth forming an accessory fruit after fertilization.In terms of anatomy,much are of the usual dicot characters such as dorsiventral leaf with stomata concentrated in the lower epidermis,eustele with pith in the stem andpresence of secondary growth both on old stem and old root.Interesting findings of the study include the123 populations,the larger leaf measurements,longer petals and larger fruits than the original description given by Matsumura.Also,the paracytic type of stomata and presence of pith in the primary roots of C.japonica subsp.intermedia are interesting since these are common monocot characters while the plant is dicot.These findings are additional information that could help clear the controversies on the genus Coriaria.More importantly,our results could provide essential information for understanding the plant and for developing conservation strategies not just for this plant but also for the other related plants in the CCR biogeographical zone.
文摘An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.
