scholarly journals Genome-wide analysis of the cupin superfamily in cowpea (Vigna unguiculata)

2020 ◽  
Author(s):  
Antônio J. Rocha ◽  
Mario Ramos de Oliveira Barsottini ◽  
Ana Luiza Sobral Paiva ◽  
José Hélio Costa ◽  
Thalles Barbosa Grangeiro
Keyword(s):  
Vigna Unguiculata ◽  
Arid Regions ◽  
Structural Features ◽  
Closely Related Species ◽  
Class A ◽  
Genome Wide ◽  
Related Plant ◽  
Multigenic Family ◽  
Cupin Superfamily ◽  
Essential Food

AbstractCowpea [Vigna unguiculata (L.)Walp.] is an essential food crop that is cultivated in many important arid and semi-arid regions of the world. In this study the genome-wide database of cowpea genes was accessed in search of genomic sequences coding for globulins, specifically members of the cupin superfamily, a well-documented multigenic family belonging to the globulin protein class. A total of seventy-seven genes belonging to the cupin superfamily were found and divided into six families. We classify V. unguiculata genes into two subgroups: classical cupins with one cupin domain (fifty-nine proteins) and bicupins with two cupin domains (eighteen members). In addition, a search for cupin members in other closely related species of the fabaceae family [V. angularis, V. radiatam and Phaseolus vulgaris (common bean)] was performed. Based on those data, a detailed characterization and comparison of the cupin genes on these species was performed with the aim to better understand the connection and functions of cupin proteins from different, but related, plant species. This study was the first attempt to investigate the cupin superfamily in V. unguiculata, allowing the identification of six cupins families and better understand the structural features of those proteins, such as number of domains alternative splicing.

scholarly journals Genome-wide analysis of the cupin superfamily in cowpea (Vigna unguiculata)

Plant Gene ◽  
2021 ◽  
Vol 25 ◽  
pp. 100265
Author(s):  
Antônio J. Rocha ◽  
José Hélio Costa ◽  
Ana Luiza Sobral Paiva ◽  
Mario Ramos de Oliveira Barsottini
Keyword(s):  
Vigna Unguiculata ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Cupin Superfamily

XVII.—The Endodermis in Light-grown and Etiolated Shoots of the Leguminosæ: A Contribution to the Causal Study of Differentiation in the Plant

1935 ◽  
Vol 58 (2) ◽  
pp. 409-425 ◽  
Author(s):  
G. Bond
Keyword(s):  
Solanum Tuberosum ◽  
Pisum Sativum ◽  
Vicia Faba ◽  
Related Species ◽  
Structural Features ◽  
Closely Related Species ◽  
Lens Esculenta ◽  
Normal Shoot ◽  
Casparian Strip ◽  
Unpublished Work

Twelve years ago Priestley and Ewing (1923) reported that in certain plants, normally showing but little development of stem-endodermis, an extensive formation of this layer could be induced by etiolation. (Note: In this paper the term endodermis is used only when the layer shows characteristic structural features—in the present case the Casparian strip.) A later paper by Priestley (1926) dealt with the same subject. The specified plants with which this result was obtained consisted of four closely related species, namely, Vicia Faba, V. sativa*, Pisum sativum, and Lens esculenta*, and also Solanum tuberosum. (The statements relating to the species marked with an asterisk are based on unpublished work carried out at Leeds, kindly placed at the author's disposal by Professor J. H. Priestley.) In these plants a primary endodermis, though present only at the base of the normal shoot, was described as extending to a considerable height in the etiolated shoot. It was concluded that the absence of endodermis from the greater part of the shoot of these plants, when grown under normal conditions, arises from the inoperation, in the presence of light, of the mechanism forming the Casparian strip.

scholarly journals Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit (Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 146
Author(s):  
Yuhong Xiong ◽  
Jing Fang ◽  
Xiaohan Jiang ◽  
Tengfei Wang ◽  
Kangchen Liu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Chloroplast Development ◽  
Structural Features ◽  
Resistance Mechanisms ◽  
Actinidia Chinensis ◽  
Rna Seq ◽  
Good Taste ◽  
Genome Wide ◽  
Solid Foundation ◽  
Chloroplast Rna

Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast development, plant growth, and response to stresses. Although the kiwifruit genome has been released, little is known about MORF genes in kiwifruit at the genome-wide level, especially those involved in the response to pathogens stress. In this study, we identified ten MORF genes in the kiwifruit genome. The genomic structures and chromosomal locations analysis indicated that all the MORF genes consisted of three conserved motifs, and they were distributed widely across the seven linkage groups and one contig of the kiwifruit genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the kiwifruit MORF gene family members were classified into six groups (Groups A–F). A synteny analysis indicated that two pairs of MORF genes were tandemly duplicated and five pairs of MORF genes were segmentally duplicated. Moreover, based on analysis of RNA-seq data from five tissues of kiwifruit, we found that both expressions of MORF genes and chloroplast RNA editing exhibited tissue-specific patterns. MORF2 and MORF9 were highly expressed in leaf and shoot, and may be responsible for chloroplast RNA editing, especially the ndhB genes. We also observed different MORF expression and chloroplast RNA editing profiles between resistant and susceptible kiwifruits after pathogen infection, indicating the roles of MORF genes in stress response by modulating the editing extend of mRNA. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes, in particular, for clarifying the resistance mechanisms in kiwifruits and breeding new cultivars with high resistance.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

scholarly journals Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species

2015 ◽  
Vol 26 (21) ◽  
pp. 3777-3787 ◽  
Author(s):  
Maike Claußen ◽  
Thomas Lingner ◽  
Claudia Pommerenke ◽  
Lennart Opitz ◽  
Gabriela Salinas ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Global Analysis ◽  
Primordial Germ Cells ◽  
Binding Studies ◽  
Closely Related Species ◽  
Cis Acting ◽  
Genome Wide ◽  
Vegetal Cortex ◽  
Gain Loss ◽  
Germ Layer Patterning

RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery.

scholarly journals Genome-wide analysis of the aquaporin genes in melon (Cucumis melo L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alvaro Lopez-Zaplana ◽  
Juan Nicolas-Espinosa ◽  
Micaela Carvajal ◽  
Gloria Bárzana
Keyword(s):  
Cucumis Melo ◽  
Evolutionary Relationship ◽  
Physiological Importance ◽  
Genome Wide ◽  
Related Plant ◽  
Complete Set ◽  
The Individual ◽  
Almost All ◽  
Relationship Of ◽  
Cucumis Melo L

AbstractMelon (Cucumis melo L.) is a very important crop throughout the world and has great economic importance, in part due to its nutritional properties. It prefers well-drained soil with low acidity and has a strong demand for water during fruit set. Therefore, a correct water balance—involving aquaporins—is necessary to maintain the plants in optimal condition. This manuscript describes the identification and comparative analysis of the complete set of aquaporins in melon. 31 aquaporin genes were identified, classified and analysed according to the evolutionary relationship of melon with related plant species. The individual role of each aquaporin in the transport of water, ions and small molecules was discussed. Finally, qPCR revealed that almost all melon aquaporins in roots and leaves were constitutively expressed. However, the high variations in expression among them point to different roles in water and solute transport, providing important features as that CmPIP1;1 is the predominant isoform and CmTIP1;1 is revealed as the most important osmoregulator in the tonoplast under optimal conditions. The results of this work pointing to the physiological importance of each individual aquaporin of melon opening a field of knowledge that deserves to be investigated.

Tracing the Evolution and Economic Potential of Konjac Glucomannan in Amorphophallus species (Araceae) using Molecular Phylogeny and RAPD Markers

Phytotaxa ◽  
2016 ◽  
Vol 282 (2) ◽  
pp. 81 ◽  
Author(s):  
ORACHORN MEKKERDCHOO ◽  
CHALEEDA BOROMPICHAICHARTKUL ◽  
ALLISON PERRIGO ◽  
GEORGE SRZEDNICKI ◽  
CHEUNJIT PRAKITCHAIWATTANA ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Its Region ◽  
Pharmaceutical Products ◽  
Konjac Glucomannan ◽  
Closely Related Species ◽  
Dna Variation ◽  
Amorphophallus Konjac ◽  
Genome Wide ◽  
Present Understanding

The genus Amorphophallus is an economically important taxon that is abundant in Old World tropical forests (Asia, Oceania and Africa). It includes many species that are used with increasing frequency as a source of food and pharmaceutical products worldwide. Amorphophallus konjac is an important economic crop and has been used widely in China and Japan for commercial konjac glucomannan (KGM) production. However, the species’ range does not extend to Thailand, where other closely related species may be more suitable for commercial KGM production. Present understanding of genetic relationships among Thai Amorphophallus species is still limited, and the connection between evolutionary history and KGM content is unknown. Here, the genetic relationships among various accessions of Amorphophallus spp. collected in Thailand are investigated using the chloroplast trnL-trnF spacer, nuclear ribosomal internal transcribed spacer (ITS) region and the second intron of LEAFY (FLint2) together with genome-wide DNA variation analysis, Randomly Amplified Polymorphic DNA (RAPD) technique. RAPD primers are also developed to quickly and efficiently identify species producing high levels of KGM. This study finds that two monophyletic clades include high KGM content species. RAPD analyses indicate that primer AC-10 generates specific bands identifying species belonging only to the high and medium KGM content clades.  These primers can be used as a screening tool for economical species, aiming at improving the industrial production of KGM in Thailand and the world.

scholarly journals Chromosome and Genome Divergence between the Cryptic Eurasian Malaria Vector-Species Anopheles messeae and Anopheles daciae

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 165 ◽  
Author(s):  
Anastasia N. Naumenko ◽  
Dmitriy A. Karagodin ◽  
Andrey A. Yurchenko ◽  
Anton V. Moskaev ◽  
Olga I. Martin ◽  
...  
Keyword(s):  
X Chromosome ◽  
Malaria Vector ◽  
Its2 Region ◽  
Nucleotide Substitutions ◽  
Closely Related Species ◽  
Chromosomal Inversions ◽  
Chromosome Inversions ◽  
Genome Wide ◽  
Genome Divergence ◽  
Incomplete Reproductive Isolation

Chromosomal inversions are important drivers of genome evolution. The Eurasian malaria vector Anopheles messeae has five polymorphic inversions. A cryptic species, An. daciae, has been discriminated from An. messeae based on five fixed nucleotide substitutions in the internal transcribed spacer 2 (ITS2) of ribosomal DNA. However, the inversion polymorphism in An. daciae and the genome divergence between these species remain unexplored. In this study, we sequenced the ITS2 region and analyzed the inversion frequencies of 289 Anopheles larvae specimens collected from three locations in the Moscow region. Five individual genomes for each of the two species were sequenced. We determined that An. messeae and An. daciae differ from each other by the frequency of polymorphic inversions. Inversion X1 was fixed in An. messeae but polymorphic in An. daciae populations. The genome sequence comparison demonstrated genome-wide divergence between the species, especially pronounced on the inversion-rich X chromosome (mean Fst = 0.331). The frequency of polymorphic autosomal inversions was higher in An. messeae than in An. daciae. We conclude that the X chromosome inversions play an important role in the genomic differentiation between the species. Our study determined that An. messeae and An. daciae are closely related species with incomplete reproductive isolation.

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