Evolutionary expansion of nematode-specific glycine-rich secreted peptides

Ying, Muying; Qiao, Yangyang; Yu, Lushan

doi:10.1016/j.gene.2016.04.049

Cited by 5 publications

(26 citation statements)

References 22 publications

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“…The number of GRSPs in each genome of the 10 species was 4 for human, 6 for zebrafish, 53 for fruit fly, 110 for C. elegans, 93 for C. briggsae, 52 for A. thaliana, 0 for M. brevicollis, 0 for S. cerevisiae, and S2 in [12]). GRSPs mature peptides are enriched for glycine with content ranging from 17 to 74% (For details, please refer to Table S3 in [12]). 62 GRSPs (30.54%) with glycine content from 30 to 40% are the most abundant (Figure 1).…”

Section: Genome-wide Analysis Of Grsps Across 10 Speciesmentioning

confidence: 99%

“…Except for Cbr-grsp-32, all the other C. briggsae GRSPs have its corresponding orthologs in C. elegans. The number of FIPR or FIP, CNC, NLP, and GRSPs family members in C. briggsae is, respectively, 31, 9, 12, and 41 (for details, please refer to Table S1 in [12]).…”

Section: Genome-wide Analysis Of Grsps Across 10 Speciesmentioning

confidence: 99%

“…Highly homologous GRSPs are usually clustered together on the two nematode genomes. This is exemplified by GRSPs from fipr-3 to fipr-9 clustered on C. elegans chromosome V. Their percent identity of protein-coding sequence ranges from 86.1 to 100% (for details, please refer to Figure S4 in [12]). It is notorious that many short genes enriched for repeat sequences are frequently incorrect in genome annotation.…”

Section: The Evidence Of Transcriptional Expression Of C Elegans Grspsmentioning

confidence: 99%

“…Evidence of transcriptional expression in GEO database showed that 65 C. elegans GRSPs were transcriptional expressions (for details, please refer to Table S1 in [12]). For the other 45 GRSPs without transcriptional evidence in GEO database, RNA reads from C. elegans transcriptome project were used to confirm their transcriptions, which showed that all GRSPs except for fipr-12 had 100% matching reads in this project (for details, please refer to Figure S5 in [12]).…”

Section: The Evidence Of Transcriptional Expression Of C Elegans Grspsmentioning

confidence: 99%

“…(for details, please refer to Table S4 in [12]). Certainly, it is possible that two C. elegans GRSPs (grsp-24 and grsp-39) without detectable expression in previous studies analyzed here may be detectable in other studies, which we were unable to mine due to the limited length of this study [7].…”

Section: Nematology -Concepts Diagnosis and Controlmentioning

confidence: 99%

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Evolutionary Expansion of Nematode-Specific Glycine-Rich Secreted Peptides

Ying¹,

Ren²,

Liu³

et al. 2017

Nematology - Concepts, Diagnosis and Control

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A genome-wide survey across 10 species from algae Guillardia theta to mammals revealed that Caenorhabditis elegans and Caenorhabditis briggsae acquired a large number of glycinerich secreted peptides (GRSPs, 110 GRSPs in C. elegans and 93 in C. briggsae) during evolution in this study. Chromosomal mapping indicated that most GRSPs were clustered on their genomes [103 (93.64%) in C. elegans and 82 (88.17%) in C. briggsae]. Totally, there are 18 GRSPs cluster units in C. elegans and 13 in C. briggsae. Except for four C. elegans where GRSP clusters lacking matching clusters in C. briggsae, all other GRSP clusters had its corresponding orthologous clusters between the two nematodes. Using eight transcriptomic datasets of Affmyetrix microarray, genome-wide association studies identified many co-expressed GRSPs clusters after C. elegans infections. Highly homologous coding sequences and conserved exon-intron organizations indicated that GRSP tight clusters might have originated from local DNA duplications. The conserved synteny blocks of GRSP clusters between their genomes, the co-expressed GRSPs clusters after C. elegans infections, and a strong purifying selection of protein-coding sequences suggested evolutionary constraint acting on C. elegans to ensure that C. elegans could rapidly launch and fulfill systematic responses against infections by co-expression, co-regulation, and co-functionality of GRSP clusters.

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Section: Genome-wide Analysis Of Grsps Across 10 Speciesmentioning

confidence: 99%

Section: Genome-wide Analysis Of Grsps Across 10 Speciesmentioning

confidence: 99%

Section: The Evidence Of Transcriptional Expression Of C Elegans Grspsmentioning

confidence: 99%

Section: The Evidence Of Transcriptional Expression Of C Elegans Grspsmentioning

confidence: 99%

Section: Nematology -Concepts Diagnosis and Controlmentioning

confidence: 99%

See 3 more Smart Citations

Evolutionary Expansion of Nematode-Specific Glycine-Rich Secreted Peptides

Ying¹,

Ren²,

Liu³

et al. 2017

Nematology - Concepts, Diagnosis and Control

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Community structure of soil nematodes under different drought conditions

Yan

Song

et al. 2018

Geoderma

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Natural variation in C. elegans short tandem repeats

Zhang

Wang

Andersen

2022

Preprint

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Short tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1-6 bp in the reference genome of C. elegans. Of these STRs, 27,636 harbored polymorphisms across 540 wild strains and only 9,691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared to the reference genome, the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed the lowest STR diversity and constrained STR mutations. STR diversity also showed similar genetic divergence and selection signatures among wild strains as in previous studies using single-nucleotide variants. We further identified STR variation in two mutation accumulation line panels that were derived from two wild strains and found background-dependent and fitness-dependent STR mutations. Overall, our results delineate the first large-scale characterization of STR variation in wild C. elegans strains and highlight the effects of selection on STR mutations.

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Evolutionary expansion of nematode-specific glycine-rich secreted peptides

Cited by 5 publications

References 22 publications

Evolutionary Expansion of Nematode-Specific Glycine-Rich Secreted Peptides

Evolutionary Expansion of Nematode-Specific Glycine-Rich Secreted Peptides

Community structure of soil nematodes under different drought conditions

Natural variation in C. elegans short tandem repeats

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