The draft genome of the parasitic nematode Trichinella spiralis

Mitreva, Makedonka; Jasmer, Douglas P.; Zarlenga, Dante S.; Wang, Zhengyuan; Abubucker, Sahar; Martin, John; Taylor, Christina; Yin, Yong; Fulton, Lucinda A.; Minx, Pat; Yang, Shiaw-Pyng; Warren, Wesley C.; Fulton, Robert S.; Bhonagiri, Veena; Zhang, Xu; Hallsworth-Pepin, Kym; Clifton, Sandra W.; McCarter, James P.; Appleton, Judith A.; Mardis, Elaine R.; Wilson, Richard K.

doi:10.1038/ng.769

Cited by 280 publications

(263 citation statements)

References 66 publications

(77 reference statements)

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“…Furthermore, the increased expression and additional targets of Ascaris 26G-RNAs may be an adaptation to the loss or changes in function of 21U-and 22G-RNA pathways. We also failed to detect piRNA pathway components in other nematode parasites of vertebrates, B. malayi and Trichinella, in which spermatogenesis also takes place at 37°C (Ghedin et al 2007;Mitreva et al 2011), further suggesting that this may be an adaption to a parasitic life cycle at higher temperatures.…”

Section: Small Rnas In Ascaris Spermatogenesismentioning

confidence: 85%

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Wang

Czech²,

Crunk³

et al. 2011

Genome Res.

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158

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Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism.

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Section: Small Rnas In Ascaris Spermatogenesismentioning

confidence: 85%

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Wang

Czech²,

Crunk³

et al. 2011

Genome Res.

Self Cite

158

189

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“…Defining gene family emergence and extinction within closely related plants can uncover the events that underlie species adaptation and cause lineage evolution (36). With multiple rice genomes now in hand, we compared SAT, NIV, GLA, BAR, GLU, MER, and BRA proteomes, and identified 39,293 orthologous gene families comprising 211,718 genes (SI Appendix, Table S29).…”

Section: Resultsmentioning

confidence: 99%

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

135

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Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.comparative genomics | full-genome sequencing | genomic variation | positive selection | Oryza D rawing the landscape of genomic divergence among multiple lineages is fundamental to understanding plant gene and genome evolution (1, 2). The comprehensive comparison of closely related genomes in different chronologically ordered stages under a well-resolved phylogenetic framework could dramatically improve the inference precision and sensitivity of gene evolution studies and should allow more robust results for investigating broad-scale patterns of genomic architecture in the course of the speciation process compared with analyses of single genomes (3, 4). For instance, studies of yeast, Drosophila, and human genomes have demonstrated how comparisons of closely related genome sequences can reveal mechanisms of gene and genome evolution in fungi and animals (5-7). In plants, however, we know little about broad-scale patterns of evolutionary dynamics, differentiation, and consequences. Studies are needed of very closely related plant species that span the speciation continuum and have well-characterized biogeographic histories.The genus Oryza, consisting of 24 species, provides a uniquely powerful system for studying comparative genomics and evolutionary biology, and can contribute to the improvement of rice, which is of pivotal significance in worldwide food production and security (8-10). Many genes involved in rice improvement are derived from wild AA-genome species, and broadening the gene pool of cultivated rice through i...

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“…1), producing a final draft assembly of 272,782,664 base pairs (bp) (N50 5 407 kilobases, kb; N90 5 80 kb; 1,618 contigs of .2 kb) ( Table 1) with a mean GC-content of 37.9%. This genome has few repetitive sequences (about 4.4% of the total assembly) relative to that reported for other metazoan genomes sequenced to date [3][4][5][6] , probably as a result of chromatin diminution 7 . We identified 424 distinct retrotransposon sequences (see Supplementary Tables 1-3) representing at least 22 families (8 long terminal repeats (LTRs), 12 long interspersed elements (LINEs) and 2 short interspersed elements (SINEs)), with Gypsy, Pao and Copia classes predominating for LTRs (n 5 97, 85 and 60, respectively) and CR1, L1, and reverse transcriptase encoding RTE-RTE classes predominating for non-LTRs (n 5 29, 28 and 21, respectively).…”

mentioning

confidence: 99%

Ascaris suum draft genome

Jex

Liu

et al. 2011

Nature

241

266

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Parasitic diseases have a devastating, long-term impact on human health, welfare and food production worldwide. More than two billion people are infected with geohelminths, including the roundworms Ascaris (common roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), mainly in developing or impoverished nations of Asia, Africa and Latin America(1). In humans, the diseases caused by these parasites result in about 135,000 deaths annually, with a global burden comparable with that of malaria or tuberculosis in disability-adjusted life years(1). Ascaris alone infects around 1.2 billion people and, in children, causes nutritional deficiency, impaired physical and cognitive development and, in severe cases, death(2). Ascaris also causes major production losses in pigs owing to reduced growth, failure to thrive and mortality(2). The Ascaris-swine model makes it possible to study the parasite, its relationship with the host, and ascariasis at the molecular level. To enable such molecular studies, we report the 273 mega-base draft genome of Ascaris suum and compare it with other nematode genomes. This genome has low repeat content (4.4%) and encodes about 18,500 protein-coding genes. Notably, the A. suum secretome (about 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissues, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases

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The draft genome of the parasitic nematode Trichinella spiralis

Cited by 280 publications

References 66 publications

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Ascaris suum draft genome

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