Orthologous Genes In Arabidopsis Research Articles

Genetic control of photoprotection and photosystem II operating efficiency in plants.

Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field-grown crops up to 40%. Using semi-high-throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize (Zea mays) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome-wide association studies. For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis (Arabidopsis thaliana) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis. Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity.

Genome-Wide Identification, Characterization, and Expression Analysis of Tubby-like Protein (TLP) Gene Family Members in Woodland Strawberry (Fragaria vesca).

Tubby-like proteins (TLPs) play important roles in plant growth and development and in responses to abiotic stress. However, TLPs in strawberry remain poorly studied. In this study, eight TLPs were identified in woodland strawberry (Fragaria vesca subspecies vesca ‘Ruegen’). Protein structure analysis revealed that the structure of FvTLPs is highly conserved, but evolutionary and gene structure analyses revealed that the evolutionary pattern of FvTLP family members differs from that of their orthologous genes in Arabidopsis, poplar, and apple. Subcellular localization assays revealed that FvTLPs were localized to the nucleus and plasma membrane. FvTLPs showed no transcriptional activity. Yeast two-hybrid assays revealed that FvTLPs interact with specific FvSKP1s. The expression patterns of FvTLPs in different tissues and under various abiotic stresses (salt, drought, cold, and heat) and hormone treatments (ABA (abscisic acid) and MeJA (methyl jasmonate)) were determined. The expression patterns of FvTLPs indicated that they play a role in regulating growth and development and responses to abiotic stress in F. vesca. The GUS (beta-glucuronidase) activity of FvTLP1pro::GUS plants in GUS activity assays increased under salt and drought stress and abscisic acid treatment. The results of this study provide new insights into the molecular mechanisms underlying the functions of TLPs.

Genome-Wide Identification and Characterization of the LpSAPK Family Genes in Perennial Ryegrass Highlight LpSAPK9 as an Active Regulator of Drought Stress.

SAPK/SnRK2 family genes play crucial roles in plant growth, development, and abiotic stress responses. The objective of this study was to identify and characterize the LpSAPK genes in perennial ryegrass (Lolium perenne L.). The results showed that there are 10 LpSAPKs in perennial ryegrass that could be classified into three groups with similar genic (exon–intron) structures to their orthologous genes in Arabidopsis and other grass species. Ka/Ks analysis suggested that the LpSAPKs and their orthologs were under purifying selection to maintain their conserved function during evolution. Nine out of ten LpSAPKs were localized in the cytoplasm and nucleus with the exception of LpSAPK5 which was only observed in the cytoplasm. Most LpSAPKs were responsive to various abiotic stress and hormonal (ABA, cytokinin, and ethylene) treatments but were downregulated in leaves and upregulated in roots, suggesting that there were unknown cis elements in promoters of these genes or unidentified post-transcriptional mechanism responsible for the tissue-dependent stress-regulated expression of these LpSAPKs. Furthermore, LpSAPK9 was identified as a candidate positive regulator in drought tolerance using a yeast ectopic expression system, and LpSAPK9 showed contrasting expression changes in drought-sensitive and -tolerant ryegrass varieties, suggesting that expression levels of LpSAPK9 were related to ryegrass drought tolerance. These results will facilitate further functional analysis of LpSAPKs for molecular breeding of ryegrass and other related grass species.

MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis

BackgroundMitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea.ResultIn this study, 5 genes of Mitogen Activated Protein Kinase Kinase (MKK) and 16 genes of Mitogen Activated Protein Kinase (MPK) in Camellia sinensis were found through a genome-wide search taking Arabidopsis thaliana as the reference genome. Also, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the results. The plant species taken for comparative study clearly displayed segmental duplication, which was a significant candidate for MAPK cascade expansion. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of MAPK and MAPKK genes from Tea in response to various abiotic factors. In addition, the expression of these genes was analysed in various tissues.ConclusionThis study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the MAPK cascade regulatory network in C. sinensis.

Comparison between the Transcriptomes of 'KDML105' Rice and a Salt-Tolerant Chromosome Segment Substitution Line.

‘KDML105’ rice, known as jasmine rice, is grown in northeast Thailand. The soil there has high salinity, which leads to low productivity. Chromosome substitution lines (CSSLs) with the ‘KDML105’ rice genetic background were evaluated for salt tolerance. CSSL18 showed the highest salt tolerance among the four lines tested. Based on a comparison between the CSSL18 and ‘KDML105’ transcriptomes, more than 27,000 genes were mapped onto the rice genome. Gene ontology enrichment of the significantly differentially expressed genes (DEGs) revealed that different mechanisms were involved in the salt stress responses between these lines. Biological process and molecular function enrichment analysis of the DEGs from both lines revealed differences in the two-component signal transduction system, involving LOC_Os04g23890, which encodes phototropin 2 (PHOT2), and LOC_Os07g44330, which encodes pyruvate dehydrogenase kinase (PDK), the enzyme that inhibits pyruvate dehydrogenase in respiration. OsPHOT2 expression was maintained in CSSL18 under salt stress, whereas it was significantly decreased in ‘KDML105’, suggesting OsPHOT2 signaling may be involved in salt tolerance in CSSL18. PDK expression was induced only in ‘KDML105’. These results suggested respiration was more inhibited in ‘KDML105’ than in CSSL18, and this may contribute to the higher salt susceptibility of ‘KDML105’ rice. Moreover, the DEGs between ‘KDML105’ and CSSL18 revealed the enrichment in transcription factors and signaling proteins located on salt-tolerant quantitative trait loci (QTLs) on chromosome 1. Two of them, OsIRO2 and OsMSR2, showed the potential to be involved in salt stress response, especially, OsMSR2, whose orthologous genes in Arabidopsis had the potential role in photosynthesis adaptation under salt stress.

Transcriptome-wide identification of WRKY family genes and their expression under cold acclimation in Eucalyptus globulus

The WRKY transcription factor family is involved in multiple biological processes, especially in the transcriptional regulation associated with plant abiotic stress response. This gene family has not been previously characterized in Eucalyptus globulus, a sensitive species to freezing temperatures, able to develop a certain degree of frost tolerance when exposed to low but nonfreezing temperatures, a phenomenon known as cold acclimation. In this study, based on the RNA-seq data from cold-acclimated E. globulus plants, a total of 51 EglWRKY genes were identified. Phylogenetic analysis allowed to classify these genes into three main groups and five subgroups, according to their putative orthologous genes in Arabidopsis. The expression patterns of 51 EglWRKY genes under cold stress were determined by in silico DEG analysis in leaf and root. Transcriptome profiling indicated that the expression of multiple EglWRKY genes is activated under chilling (4 °C) and freezing temperatures (− 6 °C). Expression patterns derived from qRT-PCR showed that 11 EglWRKY genes are regulated during cold acclimation in leaf tissue. These results provide the basis for further studies and analysis of WRKY genes to identify their function and molecular mechanisms involved in plant abiotic stress responses in E. globulus.

Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development.

The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.

Genome-wide identification, phylogeny and expression analyses of SCARECROW-LIKE(SCL) genes in millet (Setaria italica).

As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.

SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach.

Spinach (Spinacia oleracea L.), which originated in central and western Asia, belongs to the family Amaranthaceae. Spinach is one of most important leafy vegetables with a high nutritional value as well as being a perfect research material for plant sex chromosome models. As the completion of genome assembly and gene prediction of spinach, we developed SpinachDB (http://222.73.98.124/spinachdb) to store, annotate, mine and analyze genomics and genetics datasets efficiently. In this study, all of 21702 spinach genes were annotated. A total of 15741 spinach genes were catalogued into 4351 families, including identification of a substantial number of transcription factors. To construct a high-density genetic map, a total of 131592 SSRs and 1125743 potential SNPs located in 548801 loci of spinach genome were identified in 11 cultivated and wild spinach cultivars. The expression profiles were also performed with RNA-seq data using the FPKM method, which could be used to compare the genes. Paralogs in spinach and the orthologous genes in Arabidopsis, grape, sugar beet and rice were identified for comparative genome analysis. Finally, the SpinachDB website contains seven main sections, including the homepage; the GBrowse map that integrates genome, genes, SSR and SNP marker information; the Blast alignment service; the gene family classification search tool; the orthologous and paralogous gene pairs search tool; and the download and useful contact information. SpinachDB will be continually expanded to include newly generated robust genomics and genetics data sets along with the associated data mining and analysis tools.

Genetic analysis and fine mapping of the LOBED-LEAF 1 (BnLL1) gene in rapeseed (Brassica napus L.)

The lobed-leaf character is a clearly recognizable morphologic trait in rapeseed (Brassica napus L.) that has potential advantages in hybrid production. The present study was carried out to analyze the effect of lobed-leaf trait on agronomic traits and to fine map the LOBED-LEAF 1 (BnLL1) gene in B. napus. The lobed-leaf line Yuye 87 and entire-leaf cultivar Zheyou 50 were used to produce four F2 and eight BC1 populations for genetic analysis. Multiple comparison analysis between lobed-leaf character and agronomic traits was carried out in two F2 populations of reciprocal crosses between Yuye 87 and Zheyou 50. Results show that the lobed-leaf phenotype is controlled by a single an incomplete dominant gene and has no significant adverse effects on 10 main agronomic traits. The location of BnLL1 gene was narrowed down to a 36.7-kb homologous region of B. rapa between genes Bra009506 and Bra009511. On the basis of the annotation of orthologous genes in Arabidopsis, Bra009510 is considered to be a promising candidate for BnLL1 gene. The AT5G03790 is the orthologous gene of Bra009510 in Arabidopsis thaliana, with known functions in the formation of simple serrated leaves and in the suppression of bract formation. It is suggested that previously described lobed-leaf gene BnMOSAICLEAF (BnML) and the BnLL1 are the same genes controlling the lobed-leaf phenotype in B. napus, whereas the lobed-leaf gene BcLEAFLOBED 1 (BcLL1) is their homologue in Brassica campestris ssp. chinensis. These findings will facilitate the cloning and functional identification of the BnLL1 gene in future studies.

Papaya Genome: A Model for Tropical Fruit Trees and Beyond

Papaya, Carica papaya L., a major fruit crop of the tropics, is featured in a series of articles in this, the first “special issue” of Tropical Plant Biology. One of the goals of TPB is to publish occasional special issues highlighting breakthroughs on a particular plant species or unifying problem of significance in plant tropical biology. It is fitting and with pride that we devote this first special issue of TPB to one of our personally favorite tropical plants, papaya. The timing of this particular special issue is based on the April 2008 report that the papaya genome has been sequenced [2] and the release of a large set of publicly available data, which is subsequently responsible for interesting and informative research such as that being reported in this issue. This special issue highlights specific examples of how a new and interesting plant genome sequence can open new avenues to better understand angiosperm genome evolution. Papaya belongs to the order Brassicales that comprises 17 families including Caracacae, which contains papaya, and Brassicacae, the mustard or cabbage family known for its large and diverse collection of species (more than 3700 according to the Key Royal Botanical Gardens) including the model plant Arabidopsis thaliana. The placement of papaya and Arabidopsis deep within the order Brassicales allows one to use the extensive data and concepts developed extensively in Arabidopsis to discover possible gene function in papaya. More importantly, having the genome sequences of the closely related species provides information from one to help resolve unanswerable questions in the other. For example, which of the completely annotated genes of Arabidopsis are orthologs to which papaya genes? Analysis of syntenic blocks between Arabidopsis and papaya show that for single papaya genes there might be four corresponding genes in Arabidopsis [1]. The lack of multiple whole genome duplication events (polyploidy) in papaya make it a simple system for analysis and can help explain the course of genome evolution of orthologous genes in Arabidopsis. Papaya, the fifth flowering plant to be sequenced, is also the first transgenic eukaryotic organism sequenced. Having the full genome sequence of a transgenic plant allows for detailed characterization of insert size, number, site, and function for a better understanding of genetic transformation on whole genome structure and function [7]. Among the plants sequenced, papaya has the fewest functional genes, apparently as the result of undergoing only one ancient genome triplication shared by most eudicots during its evolution. Compared to the other four sequenced plant genomes, the papaya genome count of 24,746 genes is 20% fewer than that of Arabidopsis, 34% fewer than rice, 46% fewer than poplar, and 19% fewer than grape. The streamlined genome of papaya is already proving to be an excellent resource for comparative and functional analysis of both genes and repetitive elements and may provide clues about the minimum set of genes that are needed to be a flowering plant. The relative simplicity of the papaya genome makes it ideal for detailed analysis of subsets of protein coding genes that may be involved in specific physiological and biochemical processes, anatomical and morphological characteristics, or environmental sensing pathways. Each Tropical Plant Biol. (2008) 1:179–180 DOI 10.1007/s12042-008-9025-y

Axillary bud outgrowth: sending a message

Mutants that branch profusely in the presence of a growing shoot tip have highlighted the role of graft-transmissible signals that are produced in roots and stem. Orthologous genes in Arabidopsis, pea and petunia are involved in the transmission of a novel long-distance message. These genes show varying degrees of regulation by auxin and an auxin-independent feedback system, and encode enzymes that might act on carotenoid-like substrates. Axillary bud outgrowth is under homeostatic control, involving developmental stages or checkpoints. Perturbation of the long-range messaging and auxin depletion does not guarantee that bud outgrowth will ensue at a particular node.