{"title":"A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives.","authors":"Awie J Hosaka, Rena Sanetomo, Kazuyoshi Hosaka","doi":"10.1093/g3journal/jkac166","DOIUrl":"https://doi.org/10.1093/g3journal/jkac166","url":null,"abstract":"<p><p>There are over 100 known species of cultivated potatoes and their wild relatives. Many of these species, including cultivated potatoes, share the A genome; these species are mainly distributed in South America and are reproductively isolated from Mexican diploid species. The only diploid A-genome species distributed in Mexico is Solanum verrucosum Schlechtendal, which is also a maternal progenitor of Mexican polyploid species. In this study, we constructed a high-quality de novo assembly of the S. verrucosum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. A monohaploid clone (2n = x = 12) of S. verrucosum was used to reduce assembly difficulty due to the heterozygous nature of the species. The final sequence assembly consisted of 780.2 Mb of sequence, 684.0 Mb of which were anchored to the 12 chromosomes, with a scaffold N50 of 55.2 Mb. Putative centromeres were identified using publicly available data obtained via chromatin immunoprecipitation sequencing against a centromere-specific histone 3 protein. Transposable elements accounted for approximately 61.8% (482.1 Mb) of the genome, and 46,904 genes were functionally annotated. High gene synteny and similarity were revealed among the genomes of S. verrucosum, Solanum commersonii, Solanum chacoense, Solanum phureja, Solanum tuberosum, and Solanum lycopersicum. The reference-quality S. verrucosum genome will provide new insights into the evolution of Mexican polyploid species and contribute to potato breeding programs.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40463037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eva C Henningsen, Tim Hewitt, Sheshanka Dugyala, Eric S Nazareno, Erin Gilbert, Feng Li, Shahryar F Kianian, Brian J Steffenson, Peter N Dodds, Jana Sperschneider, Melania Figueroa
{"title":"A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts.","authors":"Eva C Henningsen, Tim Hewitt, Sheshanka Dugyala, Eric S Nazareno, Erin Gilbert, Feng Li, Shahryar F Kianian, Brian J Steffenson, Peter N Dodds, Jana Sperschneider, Melania Figueroa","doi":"10.1093/g3journal/jkac149","DOIUrl":"https://doi.org/10.1093/g3journal/jkac149","url":null,"abstract":"<p><p>Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40178135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Danielle L Blackwell, Sherri D Fraser, Oana Caluseriu, Claudia Vivori, Amanda V Tyndall, Ryan E Lamont, Jillian S Parboosingh, A Micheil Innes, François P Bernier, Sarah J Childs
{"title":"Hnrnpul1 controls transcription, splicing, and modulates skeletal and limb development in vivo.","authors":"Danielle L Blackwell, Sherri D Fraser, Oana Caluseriu, Claudia Vivori, Amanda V Tyndall, Ryan E Lamont, Jillian S Parboosingh, A Micheil Innes, François P Bernier, Sarah J Childs","doi":"10.1093/g3journal/jkac067","DOIUrl":"https://doi.org/10.1093/g3journal/jkac067","url":null,"abstract":"<p><p>Mutations in RNA-binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb, and neurological symptoms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are involved in nucleic acid binding, transcription, and splicing through direct binding to DNA and RNA, or through interaction with other proteins in the spliceosome. We show a developmental role for Hnrnpul1 in zebrafish, resulting in reduced body and fin growth and missing bones. Defects in craniofacial tendon growth and adult-onset caudal scoliosis are also seen. We demonstrate a role for Hnrnpul1 in alternative splicing and transcriptional regulation using RNA-sequencing, particularly of genes involved in translation, ubiquitination, and DNA damage. Given its cross-species conservation and role in splicing, it would not be surprising if it had a role in human development. Whole-exome sequencing detected a homozygous frameshift variant in HNRNPUL1 in 2 siblings with congenital limb malformations, which is a candidate gene for their limb malformations. Zebrafish Hnrnpul1 mutants suggest an important developmental role of hnRNPUL1 and provide motivation for exploring the potential conservation of ancient regulatory circuits involving hnRNPUL1 in human development.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40320487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Population differentiation and structural variation in the Manduca sexta genome across the United States.","authors":"Andrew J Mongue, Akito Y Kawahara","doi":"10.1093/g3journal/jkac047","DOIUrl":"https://doi.org/10.1093/g3journal/jkac047","url":null,"abstract":"<p><p>Many species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species' genome. Here we investigate genomic variation in 3 natural North American populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other 2 populations using Illumina whole-genome resequencing. Peaks of differentiation exist across the genome, but here, we focus in on the most striking regions. In particular, we identify 2 likely segregating inversions found in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome. The larger, 8 Mb inversion on chromosome 12 contains a pseudogene which may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to support this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for both pest management and evolutionary genetics of this insect species.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39943193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thea Mi Weiß, Xintian Zhu, Willmar L Leiser, Dongdong Li, Wenxin Liu, Wolfgang Schipprack, Albrecht E Melchinger, Volker Hahn, Tobias Würschum
{"title":"Unraveling the potential of phenomic selection within and among diverse breeding material of maize (Zea mays L.).","authors":"Thea Mi Weiß, Xintian Zhu, Willmar L Leiser, Dongdong Li, Wenxin Liu, Wolfgang Schipprack, Albrecht E Melchinger, Volker Hahn, Tobias Würschum","doi":"10.1093/g3journal/jkab445","DOIUrl":"https://doi.org/10.1093/g3journal/jkab445","url":null,"abstract":"<p><p>Genomic selection is a well-investigated approach that facilitates and supports selection decisions for complex traits and has meanwhile become a standard tool in modern plant breeding. Phenomic selection has only recently been suggested and uses the same statistical procedures to predict the targeted traits but replaces marker data with near-infrared spectroscopy data. It may represent an attractive low-cost, high-throughput alternative but has not been sufficiently studied until now. Here, we used 400 genotypes of maize (Zea mays L.) comprising elite lines of the Flint and Dent heterotic pools as well as 6 Flint landraces, which were phenotyped in multienvironment trials for anthesis-silking-interval, early vigor, final plant height, grain dry matter content, grain yield, and phosphorus concentration in the maize kernels, to compare the predictive abilities of genomic as well as phenomic prediction under different scenarios. We found that both approaches generally achieved comparable predictive abilities within material groups. However, phenomic prediction was less affected by population structure and performed better than its genomic counterpart for predictions among diverse groups of breeding material. We therefore conclude that phenomic prediction is a promising tool for practical breeding, for instance when working with unknown and rather diverse germplasm. Moreover, it may make the highly monopolized sector of plant breeding more accessible also for low-tech institutions by combining well established, widely available, and cost-efficient spectral phenotyping with the statistical procedures elaborated for genomic prediction - while achieving similar or even better results than with marker data.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8895988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39737600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elizabeth Tseng, Jason G Underwood, Brandon D Evans Hutzenbiler, Shawn Trojahn, Brewster Kingham, Olga Shevchenko, Erin Bernberg, Michelle Vierra, Charles T Robbins, Heiko T Jansen, Joanna L Kelley
{"title":"Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos).","authors":"Elizabeth Tseng, Jason G Underwood, Brandon D Evans Hutzenbiler, Shawn Trojahn, Brewster Kingham, Olga Shevchenko, Erin Bernberg, Michelle Vierra, Charles T Robbins, Heiko T Jansen, Joanna L Kelley","doi":"10.1093/g3journal/jkab422","DOIUrl":"https://doi.org/10.1093/g3journal/jkab422","url":null,"abstract":"<p><p>Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9210309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39875008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Craig H Carlson, Yongwook Choi, Agnes P Chan, Christopher D Town, Lawrence B Smart
{"title":"Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.).","authors":"Craig H Carlson, Yongwook Choi, Agnes P Chan, Christopher D Town, Lawrence B Smart","doi":"10.1093/g3journal/jkab436","DOIUrl":"https://doi.org/10.1093/g3journal/jkab436","url":null,"abstract":"<p><p>Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9210313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39874875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Erica L Larson, Emily E K Kopania, Kelsie E Hunnicutt, Dan Vanderpool, Sara Keeble, Jeffrey M Good
{"title":"Corrigendum to \"Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids\".","authors":"Erica L Larson, Emily E K Kopania, Kelsie E Hunnicutt, Dan Vanderpool, Sara Keeble, Jeffrey M Good","doi":"10.1093/g3journal/jkac007","DOIUrl":"https://doi.org/10.1093/g3journal/jkac007","url":null,"abstract":"","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8895976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39900018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yang-Tsung Lin, Tomomi Takeuchi, Brian Youk, James Umen, Barbara B Sears, Christoph Benning
{"title":"Chlamydomonas CHT7 is involved in repressing DNA replication and mitotic genes during synchronous growth.","authors":"Yang-Tsung Lin, Tomomi Takeuchi, Brian Youk, James Umen, Barbara B Sears, Christoph Benning","doi":"10.1093/g3journal/jkac023","DOIUrl":"https://doi.org/10.1093/g3journal/jkac023","url":null,"abstract":"<p><p>In the green alga Chlamydomonas reinhardtii, regulation of the cell cycle in response to external cues is critical for survival in a changing environment. The loss of the nuclear COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS 7 (CHT7) protein affects the expression of many genes especially in response to nitrogen availability. Cells lacking CHT7 exhibit abnormal cell morphology following nitrogen deprivation and fail to resume normal cell division after N resupply. To investigate the function of CHT7 in the regulation of cell cycle-related pathways, cells were synchronized, and RNA-seq analysis was performed during various stages of the cell cycle. In the cht7 mutant following nitrogen deprivation, the cells were not dividing, but a subset of cell cycle genes involved in DNA replication and mitosis were found to be derepressed, suggesting that the CHT7 protein plays a role in cell cycle regulation that is opposite to that of the mitotic cyclin-dependent kinases. Furthermore, genes for cell wall synthesis and remodeling were found to be abnormally induced in nondividing cht7 cells; this misregulation may deplete cellular resources and thus contribute to cell death following nitrogen deprivation. Lastly, 43 minimally characterized kinases were found to be highly misregulated in cht7. Further analysis suggested that some of these CHT7-regulated kinases may be related to the MAP3K and Aurora-like kinases, while others are unique. Together, these results suggest a role of CHT7 in transcriptional regulation of the cell cycle and reveal several pathways and genes whose expression appears to be subject to a CHT7-mediated regulatory network.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8895990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39902122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}