Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events

Das, Malay; Haberer, Georg; Panda, Arup; Laha, Shayani Das; Ghosh, Tapash Chandra; Schäffner, Anton R.

doi:10.1104/pp.15.01207

Cited by 50 publications

(43 citation statements)

References 44 publications

(43 reference statements)

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“…The functional redundancy of genes cannot be ruled out; however, accumulating evidence suggests that multiple CaM isoforms may have distinct and significant functions (Heo et al, 1999; Karita et al, 2004; Phean-o-pas et al, 2005; Gifford et al, 2013; Abbas et al, 2014). During the gene duplication events, there are two different kinds of homology: orthology (vertical) and paralogy (horizontal) (Das et al, 2016). Orthologs are defined as genes in different species that have originated in evolution from an ancestral gene and vertical transmission homologous genes.…”

Section: Discussionmentioning

confidence: 99%

“…Orthologs are defined as genes in different species that have originated in evolution from an ancestral gene and vertical transmission homologous genes. Orthologs frequently share the same function in the newly evolved species (Das et al, 2016). Paralog is that several homologous genes were produced by double and lateral (horizontal) of the ancestor gene in the same genome (or homologous genomes).…”

Section: Discussionmentioning

confidence: 99%

“…Paralog is that several homologous genes were produced by double and lateral (horizontal) of the ancestor gene in the same genome (or homologous genomes). The paralogs will undergo functional divergence (Das et al, 2016). Therefore, highly conserved CaM isoforms have been reported to modulate target proteins differently (Karita et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…There is no strictly definition of paralogs in function. They may be similar or different (although share a certain degree of similar structure), or even no function (such as pseudogene; Das et al, 2016). Considering that these LjCaM sequences have been conserved by natural selection, it is quite possible that these genes have significant physiological importance.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

et al. 2017

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L. japonicus, a model plant of legumes plants, is widely used in symbiotic nitrogen fixation. A large number of studies on it have been published based on the genetic, biochemical, structural studies. These results are secondhand reports that CaM is a key regulator during Rhizobial infection. In plants, there are multiple CaM genes encoding several CaM isoforms with only minor amino acid differences. Moreover, the regulation mechanism of this family of proteins during rhizobia infection is still unclear. In the current study, a family of genes encoding CaMs and CMLs that possess only the Ca2+-binding EF-hand motifs were analyzed. Using ML and BI tree based on amino acid sequence similarity, seven loci defined as CaMs and 19 CMLs, with at least 23% identity to CaM, were identified. The phylogenetics, gene structures, EF hand motif organization, and expression characteristics were evaluated. Seven CaM genes, encoding only 4 isoforms, were found in L. japonicus. According to qRT-PCR, four LjCaM isoforms are involved in different rhizobia infection stages. LjCaM1 might be involved in the early rhizobia infection epidermal cells stage. Furthermore, additional structural differences and expression behaviors indicated that LjCMLs may have different potential functions from LjCaMs.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

et al. 2017

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“…Consequently, the majority of genes are present in multiple copies. It would be important to dissect their evolutionary origin (orthologs-functional, paralogs-old/recent vs. tandem duplicates) and deduce their functional conservation or divergence by studying detailed transcriptional expression patterns (Das et al, 2016). However, the majority of these genes are very similar in sequence, which creates challenges in maintaining specificity in gene expression analyses.…”

Section: Future Challengesmentioning

confidence: 99%

Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics

et al. 2016

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Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1–120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.

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Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses

Liu

2022

The Plant Genome

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Foxtail millet [Setaria italica (L.) P. Beauv.] does not show high yield and biomass compared with maize (Zea mays L.) although it is a C 4 crop with the potential for high productivity. Because SWEET genes, which are important for sugar transport in plants, play critical roles in biomass production and seed filling in crops, genome-wide, transcriptomic, and proteomic comparison on SWEET gene family between these two species would provide some clues for unlocking this issue. In our study, 24 SWEET genes were identified in foxtail millet and maize. Sequence-based bioinformatics combined with gene expression analyses identified several candidate functional orthologs in these two species. A comparative analysis on expression characteristics of SWEET genes and proteins between maize and foxtail millet indicate that not only some critical major SWEET proteins show significant upregulation in maize compared with their orthologs in foxtail millet, but also there are more quantities of maize SWEET genes showing high expressions than that of foxtail millet genes, suggesting that compared with foxtail millet, maize possesses higher capacity of sugar transport, the crucial determinant for crop yield and biomass. These results provide a basis on revealing why foxtail millet exhibits low yield and biomass although it is a C 4 crop with the potential for high productivity. INTRODUCTIONSucrose is not only the main end product of photosynthesis but also the predominant form of photosynthates transported by the phloem in higher plants (Volkert et al., 2014).

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Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events

Cited by 50 publications

References 44 publications

Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics

Comparison of SWEET gene family between maize and foxtail millet through genomic, transcriptomic, and proteomic analyses

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