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Gene families

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Inferring defense-related gene families in Arabidopsis and wheat

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These approaches predicted up to 1790 candidate genes in 11 gene families for Arabidopsis defense to biotic stresses.

Transcriptome Analysis of Gene Families Involved in Chemosensory Function in Spodoptera littoralis (Lepidoptera: Noctuidae)

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One ex- ception is CXE8b, which has been named following CXE8 as it is a transcript variant of the same gene, shar- ing a common N terminal exon. In sum, complete ORFs are predicted for 45 of the 56 gene transcripts. CXE/CCEs display robust expression patterns in the tissues examined with ranges of abundance estimation similar to other gene families described in this report (Additional file 16).

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

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The structural diversity mainly contributed to the evolution of the gene families as indicated by evolutionary studies [64]. Taken together, these analyses suggest that the ABC transporter and HMA gene families in flax expanded over evolutionary time through gene duplication events.. A comprehensive sequence analysis of the ABC trans- porter and HMA gene families in flax was performed..

Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.)

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Identification and comprehensive analyses of the CBL and CIPK gene families in wheat (Triticum aestivum L. Comparative phylogenomics of the CBL-CIPK calcium-decoding network in the moss Physcomitrella, Arabidopsis, and other green lineages. Constitutive overexpression of the calcium sensor CBL5 confers osmotic or drought stress tolerance in Arabidopsis. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana.

Genome-wide analysis of glyoxalase-like gene families in grape (Vitis vinifera L.) and their expression profiling in response to downy mildew infection

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Sequencing of the highly homozygous grapevine PN40024 genome provided the opportunity to analyse the grapevine genome and to identify gene families [41]. Grape downy mildew, caused by the oomycete Plasmopara viticola, occurs in most parts of the world, especially in those where it is wet during the vegetative growth period. A major outbreak of the disease can cause severe losses in both yield and berry quality [42]. In this study, we identify the gene families of the glyoxalase system in V.

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

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Cassava’s PR gene responses to whiteflies were positively correlated with its response to bacteria (X. Finally, it is hoped that the genome-wide analysis of cassava’s PR gene families emphasizes the need for evalu- ating the PR gene regulatory programs in other crops to develop an understanding of the utility of PR genes as defense sentinels.. The PR genes were named according to their phylogenetic relationships in Manihot esculenta (Additional files and 16).

A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.)

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Moreover, the over-representation of families such as PcG_FIE and the under-representation of families such as C2H2 in cowpea compared to common bean and soybean is shown. and Plant Homeodomain (PHD) (184) families are the largest cowpea TF families that are under-represented with respect to common bean. When only genes and not gene models are taken into ac- count, the largest cowpea families over-represented com- pared to common bean are PcG_FIE (307), CCHC_Zn (155) and bZIP (139).

The invasive MED/Q Bemisia tabaci genome: A tale of gene loss and gene gain

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Additional file 12: Orthologous gene families specific from MEAM1/B in the MED/Q. Additional file 13: Orthologous gene families specific from others in the MED/Q. Additional file 17: Candidate PSGs in MED/Q and MEAM1/B. Gene ontology of PSG in MED/Q and MEAM1/B (FDR <.

Integrated analysis of co-expression, conserved genes and gene families reveal core regulatory network of heat stress response in Cleistogenes songorica, a xerophyte perennial desert plant

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Totals of 15, 4 and 2 homologous gene pairs were identified in the CsHSP20, CsHSP70 and CsHSP90 families, respectively.. In addition, there were 13, 2 and 2 homologous gene pairs in the CsHSP20, CsHSP70 and CsHSP90 families between subgenome A and subgenome B. We also iden- tified 24 homologous gene pairs in the CsHSF gene fam- ily, among which 14, 4 and 6 belonged to the CsHSFA, CsHSFB and CsHSFC groups, respectively (Additional file 1: Fig.

Conserved associations between Gquadruplex-forming DNA motifs and virulence gene families in malaria parasites

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Moving from the var genes to other variant gene fam- ilies, we failed to find any strong association of PQSs with any other particular gene family in the Laverania. It was not the case, for example, that the strikingly ex- panded clag families in the more ancient species all har- boured high numbers of PQSs.

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

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A comparison between the two-calculated pan-genomes revealed that 72% of the identified gene families are present in both, while 28% of the gene families (1698) identified in B. longum species are absent in the 20 newly sequenced APC/DPC genomes.

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues

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Based on 6591 gene families shown to be present in the most recent common ances- tor (MRCA) of the 10 studied plant species, our estimate for the average rate of genomic turnover was 0.0011 gains and losses per gene per million years of evolution.. In our study, 45 sequences with USPA-like domain were identified in the C. The sequences of the 1MJH-like group from C.

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

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The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals..

The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes

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To this end, I reannotated nine nematode genomes of the family Diplogastridae including seven other Pristionchus spe- cies, which were sequenced previously as part of a phy- logenomic study to investigate the evolutionary dynamics of novel gene families [9, 26].

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host

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The remaining 35 gene families searched oc- curred in at least one of the four draft genomes ana- lyzed. Out of the 40 gene families searched by TBLASTN, 35 were determined in at least one of the draft genomes analyzed. Their presence/absence indicates an intermediate size of the corresponding complement in S. hints for an intermediate comprehensiveness of the seisonid gene repertoire, as observed before in BUSCO Metazoa genes. Thus, out of the aforementioned 35 ANTP-type gene families, B.

New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

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Figure 2 showed the phylogeny of the SsCIPK gene family, which may have undergone six gene duplication events from the LCA of SsCIPK. Except for WGDs, single-gene duplicates also play an important role in the formation of gene families [51].. These observations suggest that single- gene duplication events play important roles in the ex- pansion of SsCIPK gene family in sugarcane.

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)

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We also detected another 38 TFs belonging to the gene families of SCW-biosynthesis TFs, such as PH02Gene37942 (OsMYB14), PH02Gene22729 (OSH15), and PH02Gene06702 (OsSND3) (Supplementary Table S12). The lignin-related genes covered of the enzyme gene families in the lignin biosynthesis path- way (Fig.

Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.)

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The whole genome sequence and more than 32,000 proteins of Chinese jujube have been obtained re- cently [25], which provided data resource for genome- wide analyses of specific gene families. The in- formation of MAPKs and MAPKKs of Chinese jujube is also very limited in the public databases.. Taking advantage of the available jujube genome data- base, a genome-wide search for the homologues of the MAPK and MAPKK families in jujube was performed in this study. Cloning of the ZjMPK4 gene.

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns

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However, characterizing how the gene duplicates behave differently is significant to study molecular evolution of particular gene families, and within the scope of the presented study, the fate of cyclic genes following the TGD event.

Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae

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Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae. Each paralogous group contains three homeologous copies, one in each of the A, B and D genomes with the exception of Esi3 – 2 which is missing the B copy. The Esi3 – 9 in T. The overexpression of the Z.. Members of the Esi3/RCI2/PMP3 gene families stud- ied in A.