Faculty Opinions recommendation of Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families.

2010 ◽  
Author(s):  
Nicola Mulder
Keyword(s):  
Gene Families ◽  
Cis Elements ◽  
Paralogous Gene ◽  
Specific Expression

scholarly journals Transcriptional signatures of clonally derived Toxoplasma tachyzoites reveal novel insights into the expression of a family of surface proteins.

2021 ◽  
Author(s):  
Terence Charles Theisen ◽  
John C. Boothroyd
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Toxoplasma Gondii ◽  
Gene Family ◽  
Gene Families ◽  
Surface Proteins ◽  
Paralogous Gene ◽  
Specific Expression ◽  
Related Sequence ◽  
Warm Blooded Animal

Toxoplasma gondii has numerous, large, paralogous gene families that are likely critical for supporting its unparalleled host range: nearly any nucleated cell in almost any warm-blooded animal. The SRS (SAG1-related sequence) gene family encodes over 100 proteins, the most abundant of which are thought to be involved in parasite attachment and, based on their stage-specific expression, evading the host immune response. For most SRS proteins, however, little is understood about their function and expression profile. Single-parasite RNA-sequencing previously demonstrated that across an entire population of lab-grown tachyzoites, transcripts for over 70 SRS genes were detected in at least one parasite. In any one parasite, however, transcripts for an average of only 7 SRS genes were detected, two of which, SAG1 and SAG2A , were extremely abundant and detected in virtually all. These data do not address whether this pattern of sporadic SRS gene expression is consistently inherited among the progeny of a given parasite or arises independently of lineage. We hypothesized that if SRS expression signatures are stably inherited by progeny, subclones isolated from a cloned parent would be more alike in their expression signatures than they are to the offspring of another clone. In this report, we compare transcriptomes of clonally derived parasites to determine the degree to which expression of the SRS family is stably inherited in individual parasites. Our data indicate that in RH tachyzoites, SRS genes are variably expressed even between parasite samples subcloned from the same parent within approximately 10 parasite divisions (72 hours). This suggests that the pattern of sporadically expressed SRS genes is highly variable and not driven by inheritance mechanisms, at least under our conditions.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

Novel paralogous gene families with potential function in legume nodules and seeds

2006 ◽  
Vol 9 (2) ◽  
pp. 142-146 ◽  
Author(s):  
Kevin AT Silverstein ◽  
Michelle A Graham ◽  
Kathryn A VandenBosch
Keyword(s):  
Potential Function ◽  
Gene Families ◽  
Paralogous Gene

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

scholarly journals Antennal transcriptome analyses and olfactory protein identification in an important wood-boring moth pest, Streltzoviella insularis (Lepidoptera: Cossidae)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yuchao Yang ◽  
Wenbo Li ◽  
Jing Tao ◽  
Shixiang Zong
Keyword(s):  
Protein Identification ◽  
Molecular Mechanisms ◽  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Insect Pest ◽  
Expression Patterns ◽  
Urban Forestry ◽  
Gene Families ◽  
Specific Expression ◽  
Significant Difference

AbstractOlfaction plays key roles in insect survival and reproduction, such as feeding, courtship, mating, and oviposition. The olfactory-based control strategies have been developed an important means for pest management. Streltzoviella insularis is a destructive insect pest of many street tree species, and characterization of its olfactory proteins could provide targets for the disruption of their odour recognition processes and for urban forestry protection. In this study, we assembled the antennal transcriptome of S. insularis by next-generation sequencing and annotated the main olfactory multi-gene families, including 28 odorant-binding proteins (OBPs), 12 chemosensory proteins (CSPs), 56 odorant receptors (ORs), 11 ionotropic receptors (IRs), two sensory neuron membrane proteins (SNMPs), and 101 odorant-degrading enzymes (ODEs). Sequence and phylogenetic analyses confirmed the characteristics of these proteins. We further detected tissue- and sex-specific expression patterns of OBPs, CSPs and SNMPs by quantitative real time-PCR. Most OBPs were highly and differentially expressed in the antennae of both sexes. SinsCSP10 was expressed more highly in male antennae than in other tissues. Two SNMPs were highly expressed in the antennae, with no significant difference in expression between the sexes. Our results lay a solid foundation for understanding the precise molecular mechanisms underlying S. insularis odour recognition.

scholarly journals Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 27 ◽  
Author(s):  
Sunil Sahu ◽  
Min Liu ◽  
Anna Yssel ◽  
Robert Kariba ◽  
Samuel Muthemba ◽  
...  
Keyword(s):  
Starch Synthesis ◽  
Gene Families ◽  
Genomic Information ◽  
High Quality ◽  
Specific Expression ◽  
Closely Related Species ◽  
Important Species ◽  
Specific Composition ◽  
Western Ghats Of India ◽  
The Western Ghats

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon

Genome ◽  
2019 ◽  
Vol 62 (10) ◽  
pp. 643-656 ◽  
Author(s):  
Yong Zhou ◽  
Junjie Tao ◽  
Golam Jalal Ahammed ◽  
Jingwen Li ◽  
Youxin Yang
Keyword(s):  
Expression Analysis ◽  
Developmental Stages ◽  
Plant Responses ◽  
Distribution Analysis ◽  
Cis Elements ◽  
Promoter Regions ◽  
Specific Expression ◽  
Promoter Sequences ◽  
Genome Wide ◽  
Aquaporin Gene

The plant aquaporins (AQPs) are highly conserved integral membrane proteins that participate in multiple developmental processes and responses to various stresses. In this study, a total of 35 AQP genes were identified in the watermelon genome. The phylogenetic analysis showed that these AQPs can be divided into five types, including 16 plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight nodulin 26-like intrinsic proteins (NIPs), two small basic intrinsic proteins (SIPs), and one uncategorized X intrinsic protein (XIP). A number of cis-elements related to plant responses to hormones and stresses were detected in the promoter sequences of ClAQP genes. Chromosome distribution analysis revealed that the genes are unevenly distributed on eight chromosomes, with chromosomes 1 and 4 possessing the most genes. Expression analysis at different developmental stages in flesh and rind indicated that most of ClAQPs have tissue-specific expression. Meanwhile, some other AQP genes showed differential expression in response to cold, salt, and ABA treatments, which is consistent with the organization of the stress-responsive cis-elements detected in the promoter regions. Our results lay a foundation for understanding the specific functions of ClAQP genes to help the genetic improvement of watermelon.

scholarly journals Identification and Expression Profiling of the BTB Domain-Containing Protein Gene Family in the Silkworm,Bombyx mori

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Daojun Cheng ◽  
Wenliang Qian ◽  
Meng Meng ◽  
Yonghu Wang ◽  
Jian Peng ◽  
...  
Keyword(s):  
Protein Gene ◽  
Domain Architecture ◽  
Gene Families ◽  
Monarch Butterfly ◽  
Duplication Event ◽  
Orthologous Relationship ◽  
Specific Expression ◽  
Protein Protein Interaction ◽  
Btb Domain ◽  
Silkworm Bombyx Mori

The BTB domain is a conserved protein-protein interaction motif. In this study, we identified 56 BTB domain-containing protein genes in the silkworm, in addition to 46 in the honey bee, 55 in the red flour beetle, and 53 in the monarch butterfly. Silkworm BTB protein genes were classified into nine subfamilies according to their domain architecture, and most of them could be mapped on the different chromosomes. Phylogenetic analysis suggests that silkworm BTB protein genes may have undergone a duplication event in three subfamilies: BTB-BACK-Kelch, BTB-BACK-PHR, and BTB-FLYWCH. Comparative analysis demonstrated that the orthologs of each of 13 BTB protein genes present a rigorous orthologous relationship in the silkworm and other surveyed insects, indicating conserved functions of these genes during insect evolution. Furthermore, several silkworm BTB protein genes exhibited sex-specific expression in larval tissues or at different stages during metamorphosis. These findings not only contribute to a better understanding of the evolution of insect BTB protein gene families but also provide a basis for further investigation of the functions of BTB protein genes in the silkworm.

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