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1. Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2

   https://doi.org/10.1093/g3journal/jkab364  

   Katju, Vaishali ; Konrad, Anke ; Deiss, Thaddeus C. ; Bergthorsson, Ulfar ; Félix, ed., M. -A ( October 2021 , G3 Genes|Genomes|Genetics)

   DNA mismatch repair (MMR), an evolutionarily conserved repair pathway shared by prokaryotic and eukaryotic species alike, influences molecular evolution by detecting and correcting mismatches, thereby protecting genetic fidelity, reducing the mutational load, and preventing lethality. Herein we conduct the first genome-wide evaluation of the alterations to the mutation rate and spectrum under impaired activity of the MutSα homolog, msh-2, in Caenorhabditis elegans male–female fog-2(lf) lines. We performed mutation accumulation (MA) under RNAi-induced knockdown of msh-2 for up to 50 generations, followed by next-generation sequencing of 19 MA lines and the ancestral control. msh-2 impairment in the male–female background substantially increased the frequency of nuclear base substitutions (∼23×) and small indels (∼328×) relative to wildtype hermaphrodites. However, we observed no increase in the mutation rates of mtDNA, and copy-number changes of single-copy genes. There was a marked increase in copy-number variation of rDNA genes under MMR impairment. In C. elegans, msh-2 repairs transitions more efficiently than transversions and increases the AT mutational bias relative to wildtype. The local sequence context, including sequence complexity, G + C-content, and flanking bases influenced the mutation rate. The X chromosome exhibited lower substitution and higher indel rates than autosomes, which can either result from sex-specific mutationmore »rates or a nonrandom distribution of mutable sites between chromosomes. Provided the observed difference in mutational pattern is mostly due to MMR impairment, our results indicate that the specificity of MMR varies between taxa, and is more efficient in detecting and repairing small indels in eukaryotes relative to prokaryotes.

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2. Convergent selection of a WD40 protein that enhances grain yield in maize and rice

   https://doi.org/10.1126/science.abg7985  

   Chen, Wenkang ; Chen, Lu ; Zhang, Xuan ; Yang, Ning ; Guo, Jianghua ; Wang, Min ; Ji, Shenghui ; Zhao, Xiangyu ; Yin, Pengfei ; Cai, Lichun ; et al ( March 2022 , Science)

   INTRODUCTION During the independent process of cereal evolution, many trait shifts appear to have been under convergent selection to meet the specific needs of humans. Identification of convergently selected genes across cereals could help to clarify the evolution of crop species and to accelerate breeding programs. In the past several decades, researchers have debated whether convergent phenotypic selection in distinct lineages is driven by conserved molecular changes or by diverse molecular pathways. Two of the most economically important crops, maize and rice, display some conserved phenotypic shifts—including loss of seed dispersal, decreased seed dormancy, and increased grain number during evolution—even though they experienced independent selection. Hence, maize and rice can serve as an excellent system for understanding the extent of convergent selection among cereals. RATIONALE Despite the identification of a few convergently selected genes, our understanding of the extent of molecular convergence on a genome-wide scale between maize and rice is very limited. To learn how often selection acts on orthologous genes, we investigated the functions and molecular evolution of the grain yield quantitative trait locus KRN2 in maize and its rice ortholog OsKRN2 . We also identified convergently selected genes on a genome-wide scale in maize and rice, usingmore »two large datasets. RESULTS We identified a selected gene, KRN2 ( kernel row number2 ), that differs between domesticated maize and its wild ancestor, teosinte. This gene underlies a major quantitative trait locus for kernel row number in maize. Selection in the noncoding upstream regions resulted in a reduction of KRN2 expression and an increased grain number through an increase in kernel rows. The rice ortholog, OsKRN2 , also underwent selection and negatively regulates grain number via control of secondary panicle branches. These orthologs encode WD40 proteins and function synergistically with a gene of unknown function, DUF1644, which suggests that a conserved protein interaction controls grain number in maize and rice. Field tests show that knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-off in other agronomic traits. This suggests potential applications of KRN2 and its orthologs for crop improvement. On a genome-wide scale, we identified a set of 490 orthologous genes that underwent convergent selection during maize and rice evolution, including KRN2/OsKRN2 . We found that the convergently selected orthologous genes appear to be significantly enriched in two specific pathways in both maize and rice: starch and sucrose metabolism, and biosynthesis of cofactors. A deep analysis of convergently selected genes in the starch metabolic pathway indicates that the degree of genetic convergence via convergent selection is related to the conservation and complexity of the gene network for a given selection. CONCLUSION Our findings show that common phenotypic shifts during maize and rice evolution acting on conserved genes are driven at least in part by convergent selection, which in maize and rice likely occurred both during and after domestication. We provide evolutionary and functional evidence on the convergent selection of KRN2/OsKRN2 for grain number between maize and rice. We further found that a complete loss-of-function allele of KRN2/OsKRN2 increased grain yield without an apparent negative impact on other agronomic traits. Exploring the role of KRN2/OsKRN2 and other convergently selected genes across the cereals could provide new opportunities to enhance the production of other global crops. Shared selected orthologous genes in maize and rice for convergent phenotypic shifts during domestication and improvement. By comparing 3163 selected genes in maize and 18,755 selected genes in rice, we identified 490 orthologous gene pairs, including KRN2 and its rice ortholog OsKRN2 , as having been convergently selected. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by increasing kernel rows and secondary panicle branches, respectively.« less
3. Extensive loss of Wnt genes in Tardigrada

   https://doi.org/10.1186/s12862-021-01954-y  

   Chavarria, Raul A. ; Game, Mandy ; Arbelaez, Briana ; Ramnarine, Chloe ; Snow, Zachary K. ; Smith, Frank W. ( December 2021 , BMC Ecology and Evolution)

   Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan.

   We analyzed published genomes for two representatives of Tardigrada,Hypsibius exemplarisandRamazzottius varieornatus. We identified single orthologs ofWnt4,Wnt5,Wnt9,Wnt11, andWntA, as well as twoWnt16paralogs in both tardigrade genomes. We only found aWnt2ortholog inH. exemplaris. We could not identify orthologs ofWnt1,Wnt6,Wnt7,Wnt8, orWnt10. We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog ofarrow/Lrp5/6, a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally,more »we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog ofarrow/Lrp5/6. We analyzed the embryonic expression patterns of Wnt genes inH. exemplarisduring developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes inH. exemplarisbesides one of theWnt16paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs inH. exemplaris, rather than in broadly overlapping patterns.

   Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lostWnt1,Wnt6,Wnt7,Wnt8, andWnt10, along witharrow/Lrp5/6. Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage.

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4. Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation

   https://doi.org/10.1093/molbev/msaa214  

   Kyger, Ryan ; Luzuriaga-Neira, Agusto ; Layman, Thomas ; Milkewitz Sandberg, Tatiana Orli ; Singh, Devika ; Huchon, Dorothée ; Peri, Sateesh ; Atkinson, Stephen D ; Bartholomew, Jerri L ; Yi, Soojin V ; et al ( September 2020 , Molecular Biology and Evolution)

   Saitou, Naruya (Ed.)

   Abstract DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.
5. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

   https://doi.org/10.1186/s12864-021-07967-7  

   Hong, Zhou ; Liao, Xuezhu ; Ye, Yuanjun ; Zhang, Ningnan ; Yang, Zengjiang ; Zhu, Weidong ; Gao, Wei ; Sharbrough, Joel ; Tembrock, Luke R. ; Xu, Daping ; et al ( December 2021 , BMC Genomics)

   Abstract Background Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera . Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera , the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. Results We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera . The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114more »Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. Conclusion For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.« less