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| Status |
Public on Aug 15, 2017 |
| Title |
Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris) |
| Organism |
Ascaris suum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the parasitic nematode of humans, Ascaris lumbricoides, and the parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (approximately 1000-2000 or 5%-10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline-expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent T. canis. Analysis of the chromosomal breakage regions suggests a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our genome assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies.
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| Overall design |
A total of 11 Ascaris samples are used for this study, including regions of the male germline (1, mitotic region; 2, spermatogenesis; 3, post-meiotic region; 4, seminal vesicle; and 5, spermatids), regions of the female germline (1, mitotic region; 2, early pachytene; 3, late pachytene; 4, diplotene; and 5, oocyte), and a mixed sample for 5'-end SL and TeloPrime RNA-seq.
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| Contributor(s) |
Wang J, Zagoskin M, Gao S, Davis RE |
| Citation(s) |
29118011 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 AI125869 |
Genome analysis of Ascaris programmed DNA elimination |
UNIVERSITY OF COLORADO DENVER |
Jianbin Wang |
| R01 AI049558 |
Cap-interacting proteins in metazoan trans-splicing |
UNIVERSITY OF COLORADO DENVER |
RICHARD E. DAVIS |
| R01 AI114054 |
Chromatin diminution in nematodes |
UNIVERSITY OF COLORADO DENVER |
RICHARD E. DAVIS |
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| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianbin Wang |
| E-mail(s) |
Jianbin.Wang@ucdenver.edu
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| Phone |
303-724-3227
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| Organization name |
University of Colorado Denver
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| Department |
Biochemistry and Molecular Genetics
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| Lab |
Richard E. Davis Lab
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| Street address |
12801 East 17th Ave
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (1) |
| GPL15654 |
Illumina HiSeq 2000 (Ascaris suum) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA388699 |
| SRA |
SRP108384 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99523_Ascaris.transcripts.61820.fa.gz |
23.4 Mb |
(ftp)(http) |
FA |
| GSE99523_Ascaris_transcripts_expression_reproductive.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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