More Like this

1. Developmentally regulated mitochondrial biogenesis and cell death competence in maize pollen

   https://doi.org/10.1186/s12870-022-03897-y  

   Chamusco, Karen C. ; Milazzo, May N. ; Bhan, Kanchan S. ; Kamps, Terry L. ; Smith, Prestina ; Durojaiye, Modupeoluwa ; Moreira, Cristina D. ; Gallo, Maria ; Chase, Christine D. ( November 2022 , BMC Plant Biology)

   Cytoplasmic male sterility (CMS) is a maternally inherited failure to produce functional pollen that most commonly results from expression of novel, chimeric mitochondrial genes. InZea mays, cytoplasmic male sterility type S (CMS-S) is characterized by the collapse of immature, bi-cellular pollen. Molecular and cellular features of developing CMS-S and normal (N) cytoplasm pollen were compared to determine the role of mitochondria in these differing developmental fates.

   Terminal deoxynucleotidyl transferase dUTP nick end labeling revealed both chromatin and nuclear fragmentation in the collapsed CMS-S pollen, demonstrating a programmed cell death (PCD) event sharing morphological features with mitochondria-signaled apoptosis in animals. Maize plants expressing mitochondria-targeted green fluorescent protein (GFP) demonstrated dynamic changes in mitochondrial morphology and association with actin filaments through the course of N-cytoplasm pollen development, whereas mitochondrial targeting of GFP was lost and actin filaments were disorganized in developing CMS-S pollen. Immunoblotting revealed significant developmental regulation of mitochondrial biogenesis in both CMS-S and N mito-types. Nuclear and mitochondrial genome encoded components of the cytochrome respiratory pathway and ATP synthase were of low abundance at the microspore stage, but microspores accumulated abundant nuclear-encoded alternative oxidase (AOX). Cytochrome pathway and ATP synthase components accumulated whereas AOX levels declined during the maturation of N bi-cellular pollen. Increased abundance of cytochrome pathway components and declining AOX also characterized collapsed CMS-S pollen. The accumulation and robust RNA editing of mitochondrial transcripts implicated translational or post-translational control for the developmentally regulated accumulation of mitochondria-encoded proteins in both mito-types.

   CMS-S pollen collapse is a PCD event coincident with developmentally programmed mitochondrial events including the accumulation of mitochondrial respiratory proteins and declining protection against mitochondrial generation of reactive oxygen species.

    

   more » « less
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, using 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. 

   more » « less
3. 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 114 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. 

   more » « less
4. Chromosome-level genome assembly of a regenerable maize inbred line A188

   https://doi.org/10.1186/s13059-021-02396-x  

   Lin, Guifang ; He, Cheng ; Zheng, Jun ; Koo, Dal-Hoe ; Le, Ha ; Zheng, Huakun ; Tamang, Tej Man ; Lin, Jinguang ; Liu, Yan ; Zhao, Mingxia ; et al ( June 2021 , Genome Biology)

   The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.

   Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. Highccd1expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus.

   The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

    

   more » « less
5. The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process

   https://doi.org/10.1111/nph.18966  

   Postel, Zoé ; Sloan, Daniel B. ; Gallina, Sophie ; Godé, Cécile ; Schmitt, Eric ; Mangenot, Sophie ; Drouard, Laurence ; Varré, Jean‐Stéphane ; Touzet, Pascal ( July 2023 , New Phytologist)

   There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process. In a former study, we described the possible involvement of plastid–nuclear incompatibilities in the reproductive isolation between four lineages ofSilene nutans(Caryophyllaceae). Because organellar genomes are usually cotransmitted, we assessed whether the mitochondrial genome could also be involved in the speciation process, knowing that the gynodioecious breeding system ofS. nutansis expected to impact the evolutionary dynamics of this genome.

   Using hybrid capture and high‐throughput DNA sequencing, we analyzed diversity patterns in the genic content of the organellar genomes in the fourS. nutanslineages.

   Contrary to the plastid genome, which exhibited a large number of fixed substitutions between lineages, extensive sharing of polymorphisms between lineages was found in the mitochondrial genome. In addition, numerous recombination‐like events were detected in the mitochondrial genome, loosening the linkage disequilibrium between the organellar genomes and leading to decoupled evolution.

   These results suggest that gynodioecy shaped mitochondrial diversity through balancing selection, maintaining ancestral polymorphism and, thus, limiting the involvement of the mitochondrial genome in evolution of hybrid inviability betweenS. nutanslineages.

    

   more » « less