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Wang YH, Zhao BY, Ye X, Du J, Song JL, Wang WJ, Huang XL, Ouyang KX, Zhang XQ, Liao FX, Zhong TX. Genome-wide analysis of the AP2/ERF gene family in Pennisetum glaucum and the negative role of PgRAV_01 in drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109112. [PMID: 39265240 DOI: 10.1016/j.plaphy.2024.109112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/21/2024] [Accepted: 09/06/2024] [Indexed: 09/14/2024]
Abstract
APETALA2/ethylene-responsive (AP2/ERF) plays crucial roles in resisting diverse stresses and in regulating plant growth and development. However, little is known regarding the structure and function of the AP2/ERF genes in pearl millet (Pennisetum glaucum). The AP2/ERF gene family may be involved in the development and maintenance of P. glaucum resilience to abiotic stresses, central to its role as a vital forage and cereal crop. In this study, PgAP2/ERF family members were identified and comprehensive bioinformatics analyses were performed, including determination of phylogenetic relationships, gene structures, conserved motifs, chromosomal localization, gene duplication, expression pattern, protein interaction network, and functional characterization of PgRAV_01 (Related to ABI3/VP1). In total, 78 PgAP2/ERF members were identified in the P. glaucum genome and classified into five subfamilies: AP2, ERF, DREB, RAV, and soloist. Members within the same clade of the PgAP2/ERF family showed similar gene structures and motif compositions. Six duplication events were identified in the PgAP2/ERF family; calculation of Ka/Ks values showed that purification selection dominated the evolution of PgAP2/ERFs. Subsequently, a potential interaction network of PgAP2/ERFs was generated to predict the interaction relationships. Additionally, abiotic stress expression analysis showed that most PgAP2/ERFs were induced in response to drought and heat stresses. Furthermore, overexpression of PgRAV_01 negatively regulated drought tolerance in Nicotiana benthamiana by reducing its antioxidant capacity and osmotic adjustment. Taken together, these results provide valuable insights into the characteristics and functions of PgAP2/ERF genes, with implications for abiotic stress tolerance, and will ultimately contribute to the genetic improvement of cereal crop breeding.
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Affiliation(s)
- Yin-Hua Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Grassland Science, Tianhe, Wushan Road, Guangzhou, 510642, China
| | - Bi-Yao Zhao
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Grassland Science, Tianhe, Wushan Road, Guangzhou, 510642, China
| | - Xing Ye
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Grassland Science, Tianhe, Wushan Road, Guangzhou, 510642, China
| | - Juan Du
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Jian-Ling Song
- College of biology and chemistry, Minzu Normal University of Xingyi, Xingyi, 562400, China
| | - Wen-Jing Wang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao-Ling Huang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Kun-Xi Ouyang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, 528000, China
| | - Fei-Xiong Liao
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Tian-Xiu Zhong
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Grassland Science, Tianhe, Wushan Road, Guangzhou, 510642, China.
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Boland DJ, Cornejo-Corona I, Browne DR, Murphy RL, Mullet J, Okada S, Devarenne TP. Reclassification of Botryococcus braunii chemical races into separate species based on a comparative genomics analysis. PLoS One 2024; 19:e0304144. [PMID: 39074348 DOI: 10.1371/journal.pone.0304144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/07/2024] [Indexed: 07/31/2024] Open
Abstract
The colonial green microalga Botryococcus braunii is well known for producing liquid hydrocarbons that can be utilized as biofuel feedstocks. B. braunii is taxonomically classified as a single species made up of three chemical races, A, B, and L, that are mainly distinguished by the hydrocarbons produced. We previously reported a B race draft nuclear genome, and here we report the draft nuclear genomes for the A and L races. A comparative genomic study of the three B. braunii races and 14 other algal species within Chlorophyta revealed significant differences in the genomes of each race of B. braunii. Phylogenomically, there was a clear divergence of the three races with the A race diverging earlier than both the B and L races, and the B and L races diverging from a later common ancestor not shared by the A race. DNA repeat content analysis suggested the B race had more repeat content than the A or L races. Orthogroup analysis revealed the B. braunii races displayed more gene orthogroup diversity than three closely related Chlamydomonas species, with nearly 24-36% of all genes in each B. braunii race being specific to each race. This analysis suggests the three races are distinct species based on sufficient differences in their respective genomes. We propose reclassification of the three chemical races to the following species names: Botryococcus alkenealis (A race), Botryococcus braunii (B race), and Botryococcus lycopadienor (L race).
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Affiliation(s)
- Devon J Boland
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
- Texas A&M Institute for Genome Sciences & Society (TIGSS), College Station, Texas, United States of America
| | - Ivette Cornejo-Corona
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
| | - Daniel R Browne
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
- AI & Computational Biology, LanzaTech Inc., Skokie, Illinois, United States of America
| | - Rebecca L Murphy
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
- Biology Department, Centenary College of Louisiana, Shreveport, Louisiana, United States of America
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, Japan
| | - Timothy P Devarenne
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
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Zhu J, Li T, Ma J, Li W, Zhang H, Nadezhda T, Zhu Y, Dong X, Li C, Fan J. Genome-wide identification and investigation of monosaccharide transporter gene family based on their evolution and expression analysis under abiotic stress and hormone treatments in maize (Zea mays L.). BMC PLANT BIOLOGY 2024; 24:496. [PMID: 38831278 PMCID: PMC11149190 DOI: 10.1186/s12870-024-05186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/22/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Monosaccharide transporter (MST) family, as a carrier for monosaccharide transport, plays an important role in carbon partitioning and widely involves in plant growth and development, stress response, and signaling transduction. However, little information on the MST family genes is reported in maize (Zea mays), especially in response to abiotic stresses. In this study, the genome-wide identification of MST family genes was performed in maize. RESULT A total of sixty-six putative members of MST gene family were identified and divided into seven subfamilies (including SPT, PMT, VGT, INT, pGlcT, TMT, and ERD) using bioinformatics approaches, and gene information, phylogenetic tree, chromosomal location, gene structure, motif composition, and cis-acting elements were investigated. Eight tandem and twelve segmental duplication events were identified, which played an important role in the expansion of the ZmMST family. Synteny analysis revealed the evolutionary features of MST genes in three gramineous crop species. The expression analysis indicated that most of the PMT, VGT, and ERD subfamilies members responded to osmotic and cadmium stresses, and some of them were regulated by ABA signaling, while only a few members of other subfamilies responded to stresses. In addition, only five genes were induced by NaCl stress in MST family. CONCLUSION These results serve to understand the evolutionary relationships of the ZmMST family genes and supply some insight into the processes of monosaccharide transport and carbon partitioning on the balance between plant growth and development and stress response in maize.
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Affiliation(s)
- Jialun Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Tianfeng Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Jing Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Wenyu Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Hanyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Tsyganova Nadezhda
- Saint-Petersburg State Agrarian University, Peterburgskoe shosse, Pushkin, St. Petersburg, 196601, Russia
| | - Yanshu Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning, 110866, China.
| | - Jinjuan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
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Wang H, Song J, Hunt BJ, Zuo K, Zhou H, Hayward A, Li B, Xiao Y, Geng X, Bass C, Zhou S. UDP-glycosyltransferases act as key determinants of host plant range in generalist and specialist Spodoptera species. Proc Natl Acad Sci U S A 2024; 121:e2402045121. [PMID: 38683998 PMCID: PMC11087754 DOI: 10.1073/pnas.2402045121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Phytophagous insects have evolved sophisticated detoxification systems to overcome the antiherbivore chemical defenses produced by many plants. However, how these biotransformation systems differ in generalist and specialist insect species and their role in determining insect host plant range remains an open question. Here, we show that UDP-glucosyltransferases (UGTs) play a key role in determining the host range of insect species within the Spodoptera genus. Comparative genomic analyses of Spodoptera species that differ in host plant breadth identified a relatively conserved number of UGT genes in generalist species but high levels of UGT gene pseudogenization in the specialist Spodoptera picta. CRISPR-Cas9 knockouts of the three main UGT gene clusters of Spodoptera frugiperda revealed that UGT33 genes play an important role in allowing this species to utilize the poaceous plants maize, wheat, and rice, while UGT40 genes facilitate utilization of cotton. Further functional analyses in vivo and in vitro identified the UGT SfUGT33F32 as the key mechanism that allows generalist S. frugiperda to detoxify the benzoxazinoid DIMBOA (2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one), a potent insecticidal phytotoxin produced by poaceous plants. However, while this detoxification capacity is conserved in several generalist Spodoptera species, Spodoptera picta, which specializes on Crinum plants, is unable to detoxify DIMBOA due to a nonfunctionalizing mutation in SpUGT33F34. Collectively, these findings provide insight into the role of insect UGTs in host plant adaptation, the mechanistic basis of evolutionary transitions between generalism and specialism and offer molecular targets for controlling a group of notorious insect pests.
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Affiliation(s)
- Huidong Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Jing Song
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Benjamin J. Hunt
- Centre for Ecology and Conservation, University of Exeter, PenrynTR10 9FE, United Kingdom
| | - Kairan Zuo
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Huiru Zhou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Angela Hayward
- Centre for Ecology and Conservation, University of Exeter, PenrynTR10 9FE, United Kingdom
| | - Bingbing Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Yajuan Xiao
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Xing Geng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, PenrynTR10 9FE, United Kingdom
| | - Shutang Zhou
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Life Sciences, College of Agriculture, Henan University, Kaifeng475004, Henan, China
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Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
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Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
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Gozashti L, Hartl DL, Corbett-Detig R. Universal signatures of transposable element compartmentalization across eukaryotic genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.17.562820. [PMID: 38585780 PMCID: PMC10996525 DOI: 10.1101/2023.10.17.562820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity1,2. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression3. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Scanlan JL, Robin C. Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification. Genome Biol Evol 2024; 16:evae019. [PMID: 38291829 PMCID: PMC10859841 DOI: 10.1093/gbe/evae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid molting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown, and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and we also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. Our evolutionary analyses provide hypotheses of function and a robust framework for future experimental studies of the EcKL gene family. They also open promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied coevolution of butterflies with their host plants.
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Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Rosani U, De Felice S, Frizzo R, Kawato S, Wegner KM. FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses. Gene 2024; 893:147895. [PMID: 37832807 DOI: 10.1016/j.gene.2023.147895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs). FicDs catalyze AMPylation, a post-translational protein modification consisting in the addition of adenosine monophosphate to accessible residues of target proteins. Beside the well-known conservation of FicDs in deuterostomes, we report the presence of a conserved FicD gene ortholog in a large number of protostomes and microbial eukaryotes. We also reported additional FicD gene copies in the genomes of some rotifers, parasitic worms and bivalves. A few dsDNA viruses of these invertebrates, including White spot syndrome virus, Cherax quadricarinatus iridovirus, Ostreid herpesvirus-1 and the beetle nudivirus, carry copies of FicDs, with phylogenetic analysis suggesting a common origin of these FicD copies and the duplicated FicDs of their invertebrate hosts. HGTs and gene duplications possibly mediated by endogenous viruses or genetic mobile elements seem to have contributed to the transfer of AMPylation ability from bacteria and eukaryotes to pathogenic viruses, where this pathway could have been hijacked to promote viral infection.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Sofia De Felice
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Riccardo Frizzo
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, 108-8477 Tokyo, Japan
| | - K Mathias Wegner
- Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, Waddensea Station Sylt, 25992 List, Germany
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Sharma SP, Purcell CM, Hyde JR, Severin AJ. Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales. Int J Syst Evol Microbiol 2024; 74. [PMID: 38179990 DOI: 10.1099/ijsem.0.006198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone (Haliotis rufescens) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae. We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone (Haliotis sorenseni). In addition, we highlight the need for better classification of taxa within the class Spirochaetia.
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Affiliation(s)
| | - Catherine M Purcell
- NOAA Fisheries Southwest Fisheries Science Center, La Jolla, California, USA
| | - John R Hyde
- NOAA Fisheries Southwest Fisheries Science Center, La Jolla, California, USA
| | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Ames, Iowa, USA
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Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
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Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Mol Ecol 2023. [PMID: 37843462 DOI: 10.1111/mec.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty means that they evade reconstruction by the classical tools of evolutionary modelling. This evasion of deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of lineage-specific genes (LSGs). Using gene synteny, we documented that 78% of Neurospora LSG clusters are located adjacent to the telomeres featuring extensive tracts of non-coding DNA and duplicated genes. Here, we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate the functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of the LSG mas-1, a gene with roles in cell-wall integrity and cellular sensitivity to antifungal toxins, was investigated in detail alongside its genomic neighbours, indicating that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. Our discoveries illuminate a "rummage region" in the N. crassa genome that enables the formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by sequence repeats and unconstrained non-coding sequences.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, Davis, California, USA
| | - Hayley Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
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12
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Tasleem M, Hussein WM, El-Sayed AAAA, Alrehaily A. An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals in Pseudomonas aeruginosa. Microorganisms 2023; 11:2262. [PMID: 37764106 PMCID: PMC10537150 DOI: 10.3390/microorganisms11092262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Microorganisms are ubiquitously present in the environment and exert significant influence on numerous natural phenomena. The soil and groundwater systems, precipitation, and effluent outfalls from factories, refineries, and waste treatment facilities are all sources of heavy metal contamination. For example, Madinah, Saudi Arabia, has alarmingly high levels of lead and cadmium. The non-essential minerals cadmium (Cd) and lead (Pb) have been linked to damage to vital organs. Bioremediation is an essential component in the process of cleaning up polluted soil and water where biological agents such as bacteria are used to remove the contaminants. It is demonstrated that Pseudomonas aeruginosa (P. aeruginosa) isolated from activated sludge was able to remove Cd and Pb from water. The protein sequence of metallothionein from P. aeruginosa was retrieved to explore it for physicoparameters, orthologs, domain, family, motifs, and conserved residues. The homology structure was generated, and models were validated. Docking of the best model with the heavy metals was carried out to inspect the intramolecular interactions. The target protein was found to belong to the "metallothionein_pro" family, containing six motifs, and showed a close orthologous relationship with other heavy metal-resistant bacteria. The best model was generated by Phyre2. In this study, three key residues of metallothionein were identified that participate in heavy metal (Pb and Cd) binding, viz., Ala33, Ser34, and Glu59. In addition, the study provides an essential basis to explore protein engineering for the optimum use of metallothionein protein to reduce/remove heavy metals from the environment.
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Affiliation(s)
- Munazzah Tasleem
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
| | - Wesam M. Hussein
- Chemistry Department, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia;
| | | | - Abdulwahed Alrehaily
- Biology Department, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia;
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13
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Chen H, Zhang Y, Feng S. Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages. BMC Genomics 2023; 24:290. [PMID: 37254040 DOI: 10.1186/s12864-023-09389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages. RESULTS Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations. CONCLUSIONS This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yingchao Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Shuyan Feng
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
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14
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Ortiz J, Bobkov YV, DeBiasse MB, Mitchell DG, Edgar A, Martindale MQ, Moss AG, Babonis LS, Ryan JF. Independent Innexin Radiation Shaped Signaling in Ctenophores. Mol Biol Evol 2023; 40:7026321. [PMID: 36740225 PMCID: PMC9949713 DOI: 10.1093/molbev/msad025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/30/2022] [Accepted: 01/25/2023] [Indexed: 02/07/2023] Open
Abstract
Innexins facilitate cell-cell communication by forming gap junctions or nonjunctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here, we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggests that this cluster has been maintained due to constraints related to gene regulation. We describe the basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.
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Affiliation(s)
| | | | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Anthony G Moss
- Biological Sciences Department, Auburn University, Auburn, AL, USA
| | - Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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15
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You Y, Sun X, Lin S. An ancient enzyme finds a new home: Prevalence and neofunctionalization of trypsin in marine phytoplankton. JOURNAL OF PHYCOLOGY 2023; 59:152-166. [PMID: 36369667 DOI: 10.1111/jpy.13300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Trypsin is an ancient protease best known as a digestive enzyme in animals, and traditionally believed to be absent in plants and protists. However, our recent studies have revealed its wide presence and important roles in marine phytoplankton. Here, to gain a better understanding on the importance of trypsin in phytoplankton, we further surveyed the distribution, diversity, evolution and potential ecological roles of trypsin in global ocean phytoplankton. Our analysis indicated that trypsin is widely distributed both taxonomically and geographically in marine phytoplankton. Furthermore, by systematic comparative analyses we found that algal trypsin could be classified into two subfamilies (trypsin I and trypsin II) and exhibited highly duplicated and diversified during evolution. We also observed markedly different domain sequences and organizations between and within the subfamilies, suggesting potential neofunctionalization. Diatoms contain both subfamilies of trypsin, with higher numbers of genes and more environment-responsive expression of trypsin than other lineages. The duplication and subsequent neofunctionalization of the trypsin family may be important in diatoms for adapting to dynamical environmental conditions, contributing to diatoms' dominance in the coastal oceans. This work advances our knowledge on the distribution and neofunctionalization of this ancient enzyme and creates a new window of research on phytoplankton biology.
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Affiliation(s)
- Yanchun You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, 266237, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340-6048, USA
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16
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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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17
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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18
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Rebholz Z, Lancaster J, Larose H, Khrimian A, Luck K, Sparks ME, Gendreau KL, Shewade L, Köllner TG, Weber DC, Gundersen-Rindal DE, O'Maille P, Morozov AV, Tholl D. Ancient origin and conserved gene function in terpene pheromone and defense evolution of stink bugs and hemipteran insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 152:103879. [PMID: 36470318 DOI: 10.1016/j.ibmb.2022.103879] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Insects use diverse arrays of small molecules such as metabolites of the large class of terpenes for intra- and inter-specific communication and defense. These molecules are synthesized by specialized metabolic pathways; however, the origin of enzymes involved in terpene biosynthesis and their evolution in insect genomes is still poorly understood. We addressed this question by investigating the evolution of isoprenyl diphosphate synthase (IDS)-like genes with terpene synthase (TPS) function in the family of stink bugs (Pentatomidae) within the large order of piercing-sucking Hemipteran insects. Stink bugs include species of global pest status, many of which emit structurally related 15-carbon sesquiterpenes as sex or aggregation pheromones. We provide evidence for the emergence of IDS-type TPS enzymes at the onset of pentatomid evolution over 100 million years ago, coinciding with the evolution of flowering plants. Stink bugs of different geographical origin maintain small IDS-type families with genes of conserved TPS function, which stands in contrast to the diversification of TPS genes in plants. Expanded gene mining and phylogenetic analysis in other hemipteran insects further provides evidence for an ancient emergence of IDS-like genes under presumed selection for terpene-mediated chemical interactions, and this process occurred independently from a similar evolution of IDS-type TPS genes in beetles. Our findings further suggest differences in TPS diversification in insects and plants in conjunction with different modes of gene functionalization in chemical interactions.
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Affiliation(s)
- Zarley Rebholz
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Jason Lancaster
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Hailey Larose
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Ashot Khrimian
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Katrin Luck
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745, Jena, Germany
| | - Michael E Sparks
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Kerry L Gendreau
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Leena Shewade
- SRI International, Biosciences Division, 333 Ravenswood Avenue, Menlo Park, CA, 94025-3493, USA
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745, Jena, Germany
| | - Donald C Weber
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Dawn E Gundersen-Rindal
- Invasive Insect Biocontrol and Behavior Laboratory, USDA Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Paul O'Maille
- SRI International, Biosciences Division, 333 Ravenswood Avenue, Menlo Park, CA, 94025-3493, USA
| | - Alexandre V Morozov
- Department of Physics & Astronomy and Center for Quantitative Biology, Rutgers University, 136 Frelinghuysen Rd., Piscataway, NJ, 08854-8019, USA
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA.
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19
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Kesawat MS, Kherawat BS, Ram C, Singh A, Dey P, Gora JS, Misra N, Chung SM, Kumar M. Genome-Wide Identification and Expression Profiling of Aconitase Gene Family Members Reveals Their Roles in Plant Development and Adaptation to Diverse Stress in Triticum aestivum L. PLANTS 2022; 11:3475. [PMID: 36559588 PMCID: PMC9782157 DOI: 10.3390/plants11243475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 06/01/2023]
Abstract
Global warming is a serious threat to food security and severely affects plant growth, developmental processes, and, eventually, crop productivity. Respiratory metabolism plays a critical role in the adaptation of diverse stress in plants. Aconitase (ACO) is the main enzyme, which catalyzes the revocable isomerization of citrate to isocitrate in the Krebs cycle. The function of ACO gene family members has been extensively studied in model plants, for instance Arabidopsis. However, their role in plant developmental processes and various stress conditions largely remained unknown in other plant species. Thus, we identified 15 ACO genes in wheat to elucidate their function in plant developmental processes and different stress environments. The phylogenetic tree revealed that TaACO genes were classified into six groups. Further, gene structure analysis of TaACOs has shown a distinctive evolutionary path. Synteny analysis showed the 84 orthologous gene pairs in Brachypodium distachyon, Aegilops tauschii, Triticum dicoccoides, Oryza sativa, and Arabidopsis thaliana. Furthermore, Ka/Ks ratio revealed that most TaACO genes experienced strong purifying selection during evolution. Numerous cis-acting regulatory elements were detected in the TaACO promoters, which play a crucial role in plant development processes, phytohormone signaling, and are related to defense and stress. To understand the function of TaACO genes, the expression profiling of TaACO genes were investigated in different tissues, developmental stages, and stress conditions. The transcript per million values of TaACOs genes were retrieved from the Wheat Expression Browser Database. We noticed the differential expression of the TaACO genes in different tissues and various stress conditions. Moreover, gene ontology analysis has shown enrichment in the tricarboxylic acid metabolic process (GO:0072350), citrate metabolic process (GO:0006101), isocitrate metabolic process GO:0006102, carbohydrate metabolic (GO:0005975), and glyoxylate metabolic process (GO:0046487). Therefore, this study provided valuable insight into the ACO gene family in wheat and contributed to the further functional characterization of TaACO during different plant development processes and various stress conditions.
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Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, India
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, India
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, India
| | - Anupama Singh
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, India
| | - Prajjal Dey
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, India
| | - Jagan Singh Gora
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology 13 (KIIT), Deemed to be University, Bhubaneswar 751024, India
| | - Sang-Min Chung
- Department of Life Science, Dongguk University, Dong-gu 10326, Republic of Korea
| | - Manu Kumar
- Department of Life Science, Dongguk University, Dong-gu 10326, Republic of Korea
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20
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Patil AB, Vajja SS, Raghavendra S, Satish BN, Kushalappa CG, Vijay N. Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus. FRONTIERS IN PLANT SCIENCE 2022; 13:1029540. [PMID: 36578332 PMCID: PMC9791056 DOI: 10.3389/fpls.2022.1029540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Sai Samhitha Vajja
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - S. Raghavendra
- College of Agriculture Hassan, University of Agricultural Sciences (UAS), Bangalore, Karnataka, India
| | - B. N. Satish
- College of Forestry, Ponnampet, Karnataka, India
| | | | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
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21
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Bano N, Aalam S, Bag SK. Tubby-like proteins (TLPs) transcription factor in different regulatory mechanism in plants: a review. PLANT MOLECULAR BIOLOGY 2022; 110:455-468. [PMID: 36255595 DOI: 10.1007/s11103-022-01301-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023]
Abstract
Tubby-like proteins (TLPs) transcription factors are found in single-celled to multi-cellular eukaryotes in the form of large multigene families. TLPs are identified through a specific signature of carboxyl terminal tubby domain, required for plasma membrane tethering and amino terminal F-box domain communicate as functional SCF-type E3 ligases. The comprehensive distribution of TLP gene family members in diverse species indicates some conserved functions of TLPs in multicellular organisms. Plant TLPs have higher gene members than animals and these members reported important role in multiple physiological and developmental processes and various environmental stress responses. Although the TLPs are suggested to be a putative transcription factors but their functional mechanism is not much clear. This review provides significant recent updates on TLP-mediated regulation with an insight into its functional roles, origin and evolution and also phytohormones related regulation to combat with various stresses and its involvement in adaptive stress response in crop plants.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahre Aalam
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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22
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Liu Z, Xing L, Huang W, Liu B, Wan F, Raffa KF, Hofstetter RW, Qian W, Sun J. Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens. BMC Biol 2022; 20:190. [PMID: 36002826 PMCID: PMC9400205 DOI: 10.1186/s12915-022-01388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.
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Affiliation(s)
- Zhudong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China
| | - Longsheng Xing
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | | | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kenneth F Raffa
- Department of Entomology, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Jianghua Sun
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China.
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23
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Kwak Y, Argandona JA, Degnan PH, Hansen AK. Chromosomal-level assembly of Bactericera cockerelli reveals rampant gene family expansions impacting genome structure, function and insect-microbe-plant-interactions. Mol Ecol Resour 2022; 23:233-252. [PMID: 35925827 PMCID: PMC10087415 DOI: 10.1111/1755-0998.13693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022]
Abstract
Lineage specific expansions and gene duplications are some of the most important sources of evolutionary novelty in eukaryotes. Although not as prevalent in eukaryotes compared to bacteria, horizontal gene transfer events can also result in key adaptations for insects, especially for those involved in insect-microbe interactions. In this study we assemble the first chromosomal assembly of the psyllid Bactericera cockerelli and reveal that the B. cockerelli genome has experienced significantly more gene expansion events compared to other Hemipteran representatives with fully sequenced genomes. We also reveal that B. cockerelli's genome is the largest psyllid genome (567 Mb) sequenced to date and is ~15% larger than the other two psyllid species genomes sequenced (Pachypsylla venusta and Diaphorina citri). Structurally, B. cockerelli appears to have an additional chromosome compared to the distantly related psyllid species P. venusta due to a previous chromosomal fission or fusion event. The increase in genome size and dynamic nature of the B. cockerelli genome may largely be contributed to the widespread expansion of type I and type II repeat elements that are rampant across all of B. cockerelli's. chromosomes. These repeat elements are distributed near equally in both euchromatic and heterochromatic regions. Furthermore, significant gene family expansions and gene duplications were uncovered for genes that are expected to be important in its adaptation to insect-plant and microbe interactions, which include transcription factors, proteases, odorant receptors, and horizontally transferred genes that are involved in the nutritional symbioses with their long-term nutritional endosymbiont Carsonella.
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Affiliation(s)
- Younghwan Kwak
- Department of Entomology, University of California, CA, USA
| | | | - Patrick H Degnan
- Department of Microbiology and Plant Pathology, University of California, CA, USA
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24
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Li M, Wang Y, Tang Z, Wang H, Hu J, Bao Z, Hu X. Expression Plasticity of Peroxisomal Acyl-Coenzyme A Oxidase Genes Implies Their Involvement in Redox Regulation in Scallops Exposed to PST-Producing Alexandrium. Mar Drugs 2022; 20:md20080472. [PMID: 35892940 PMCID: PMC9332717 DOI: 10.3390/md20080472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/10/2022] Open
Abstract
Filter-feeding bivalves can accumulate paralytic shellfish toxins (PST) produced by toxic microalgae, which may induce oxidative stress and lipid peroxidation. Peroxisomal acyl-coenzyme A oxidases (ACOXs) are key enzymes functioning in maintaining redox and lipid homeostasis, but their roles in PST response in bivalves are less understood. Herein, a total of six and six ACOXs were identified in the Chlamys farreri and Patinopecten yessoensis genome, respectively, and the expansion of ACOX1s was observed. Gene expression analysis revealed an organ/tissue-specific expression pattern in both scallops, with all ACOXs being predominantly expressed in the two most toxic organs, digestive glands and kidneys. The regulation patterns of scallop ACOXs after exposure to different PST-producing algaes Alexandrium catenella (ACDH) and A. minutum (AM-1) were revealed. After ACDH exposure, more differentially expressed genes (DEGs) were identified in C. farreri digestive glands (three) and kidneys (five) than that in P. yessoensis (two), but the up-regulated DEGs showed similar expression patterns in both species. In C. farreri, three DEGs were found in both digestive glands and kidneys after AM-1 exposure, with two same CfACOX1s being acutely and chronically induced, respectively. Notably, these two CfACOX1s also showed different expression patterns in kidneys between ACDH (acute response) and AM-1 (chronic response) exposure. Moreover, inductive expression of CfACOXs after AM-1 exposure was observed in gills and mantles, and all DEGs in both tissues were up-regulated and their common DEGs exhibited both acute and chronic induction. These results indicate the involvement of scallop ACOXs in PST response, and their plasticity expression patterns between scallop species, among tissues, and between the exposure of different PST analogs.
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Affiliation(s)
- Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
| | - Yangrui Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
| | - Zhihong Tang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
| | - Huizhen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: ; Tel.: +86-0532-8203-1970
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (M.L.); (Y.W.); (Z.T.); (J.H.); (Z.B.); (X.H.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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25
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Holden S, Bergum M, Green P, Bettgenhaeuser J, Hernández-Pinzón I, Thind A, Clare S, Russell JM, Hubbard A, Taylor J, Smoker M, Gardiner M, Civolani L, Cosenza F, Rosignoli S, Strugala R, Molnár I, Šimková H, Doležel J, Schaffrath U, Barrett M, Salvi S, Moscou MJ. A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley. SCIENCE ADVANCES 2022; 8:eabn7258. [PMID: 35857460 PMCID: PMC9258809 DOI: 10.1126/sciadv.abn7258] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity but lack causal association. Here, we show that Rps8-mediated resistance in barley to the pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: Pur1 and Exo70FX12, which are together necessary and sufficient. Pur1 encodes a leucine-rich repeat receptor kinase and is the ortholog of rice Xa21, and Exo70FX12 belongs to the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Pur1-mediated immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.
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Affiliation(s)
- Samuel Holden
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Molly Bergum
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jan Bettgenhaeuser
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Anupriya Thind
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shaun Clare
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - James M. Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Amelia Hubbard
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, England, UK
| | - Jodi Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Gardiner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laura Civolani
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Francesco Cosenza
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Serena Rosignoli
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Roxana Strugala
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - István Molnár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Matthew Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield 4878, Australia
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Matthew J. Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Corresponding author.
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26
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Ahmad MZ, Shah Z, Ullah A, Ahmed S, Ahmad B, Khan A. Genome wide and evolutionary analysis of heat shock protein 70 proteins in tomato and their role in response to heat and drought stress. Mol Biol Rep 2022; 49:11229-11241. [PMID: 35788950 DOI: 10.1007/s11033-022-07734-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/22/2022] [Indexed: 11/24/2022]
Abstract
Heat shock protein 70 (HSP70) proteins play a crucial role in mitigating the detrimental effects of abiotic stresses in plants. In the present study, 21 full length non-redundant SlHSP70 genes were detected and characterized in tomato (Solanum lycopersicum L.). The SlHSP70 genes were classified into four groups based on phylogenetic analysis. Similarities were observed in gene features and motif structures of SlHSP70s belonging to the same group. SlHSP70 genes were unevenly and unequally mapped on 11 chromosomes. Segmental and tandem duplication are the main events that have contributed to the expansion of the SlHSP70 genes. A large number of groups and sub-groups were generated during comparative analysis of HSP70 genes in multiple plant species including tomato. These findings indicated a common ancestor which created diverse sub-groups prior to a mono-dicot split. The selection pressure on specific codons was identified through a maximum-likelihood approach and we found some important coding sites in the coding region of all groups. Diversifying positive selection was indirectly associated with evolutionary changes in SlHSP70 proteins and suggests that gene evolution modulated the tomato domestication event. In addition, expression analysis using RNA-seq revealed that 21 SlHSP70 genes were differentially expressed in response to drought and heat stress. SlHSP70-5 was down-regulated by heat treatment and up-regulated by drought stress. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. Our results indicate the diverse role of HSP70 gene family in S. lycopersicum under drought and heat stress conditions and open the gate for further investigation of HSP70 gene family functions, especially under drought and heat stress.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture, D.I. Khan, Pakistan.
| | - Zamarud Shah
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Arif Ullah
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Shakeel Ahmed
- Institute de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, 5090000, Valdivia, Chile
| | - Bushra Ahmad
- Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Afrasyab Khan
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
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27
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Herath V, Connolly K, Roach A, Ausekar A, Persky T, Verchot J. The plant endoplasmic reticulum UPRome: A repository and pathway browser for genes involved in signaling networks linked to the endoplasmic reticulum. PLANT DIRECT 2022; 6:e431. [PMID: 35875835 PMCID: PMC9300056 DOI: 10.1002/pld3.431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The endoplasmic reticulum (ER) houses sensors that respond to environmental stress and underly plants' adaptative responses. These sensors transduce signals that lead to changes in nuclear gene expression. The ER to nuclear signaling pathways are primarily attributed to the unfolded protein response (UPR) and are also integrated with a wide range of development, hormone, immune, and stress signaling pathways. Understanding the role of the UPR in signaling network mechanisms that associate with particular phenotypes is crucially important. While UPR-associated genes are the subject of ongoing investigations in a few model plant systems, most remain poorly annotated, hindering the identification of candidates across plant species. This open-source curated database provides a centralized resource of peer reviewed knowledge of ER to nuclear signaling pathways for the plant community. We provide a UPRome interactive viewer for users to navigate through the pathways and to access annotated information. The plant ER UPRome website is located at http://uprome.tamu.edu. We welcome contributions from the researchers studying the ER UPR to incorporate additional genes into the database through the "contact us" page.
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Affiliation(s)
- Venura Herath
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
- Department of Agriculture Biology, Faculty of AgricultureUniversity of PeridaniyaPeradeniyaSri Lanka
| | - Kaylee Connolly
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
| | - Anna Roach
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
| | - Ashish Ausekar
- Division of Information TechnologyTexas A&M UniversityCollege StationTexasUSA
| | - Tracy Persky
- Division of Information TechnologyTexas A&M UniversityCollege StationTexasUSA
| | - Jeanmarie Verchot
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
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28
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E2 ubiquitin-conjugating enzymes (UBCs): drivers of ubiquitin signalling in plants. Essays Biochem 2022; 66:99-110. [PMID: 35766526 DOI: 10.1042/ebc20210093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/22/2022]
Abstract
Most research in the field of ubiquitination has focused on E3 ubiquitin ligases because they are the specificity determinants of the ubiquitination process. Nevertheless, E2s are responsible for the catalysis during ubiquitin transfer, and are therefore, at the heart of the ubiquitination process. Arabidopsis has 37 ubiquitin E2s with additional ones mediating the attachment of ubiquitin-like proteins (e.g. SUMO, Nedd8 and ATG8). Importantly, E2s largely determine the type of ubiquitin chain built, and therefore, the type of signal that decides over the fate of the modified protein, such as degradation by the proteasome (Lys48-linked ubiquitin chains) or relocalization (Lys63-linked ubiquitin chains). Moreover, new regulatory layers impinging on E2s activity, including post-translational modifications or cofactors, are emerging that highlight the importance of E2s.
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29
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Zhou G, Liu C, Cheng Y, Ruan M, Ye Q, Wang R, Yao Z, Wan H. Molecular Evolution and Functional Divergence of Stress-Responsive Cu/Zn Superoxide Dismutases in Plants. Int J Mol Sci 2022; 23:7082. [PMID: 35806085 PMCID: PMC9266695 DOI: 10.3390/ijms23137082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/25/2022] Open
Abstract
Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved in many of the biological functions of plants in response to abiotic and biotic stresses. Here, we carried out a comprehensive analysis of the Cu/Zn SOD gene family in different plant species, ranging from lower plants to higher plants, and further investigated their organization, sequence features, and expression patterns in response to biotic and abiotic stresses. Our results show that plant Cu/Zn SODs can be divided into two subfamilies (group I and group II). Group II appeared to be conserved only as single- or low-copy genes in all lineages, whereas group I genes underwent at least two duplication events, resulting in multiple gene copies and forming three different subgroups (group Ia, group Ib, and group Ic). We also found that, among these genes, two important events-the loss of introns and the loss of and variation in signal peptides-occurred over the long course of their evolution, indicating that they were involved in shifts in subcellular localization from the chloroplast to cytosol or peroxisome and underwent functional divergence. In addition, expression patterns of Cu/Zn SOD genes from Arabidopsis thaliana and Solanum lycopersicum were tested in different tissues/organs and developmental stages and under different abiotic stresses. The results indicate that the Cu/Zn SOD gene family possesses potential functional divergence and may play vital roles in ROS scavenging in response to various stresses in plants. This study will help establish a foundation for further understanding these genes' function during stress responses.
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Affiliation(s)
- Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Chaochao Liu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212021, China;
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Meiying Ruan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Qingjing Ye
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Zhuping Yao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (M.R.); (Q.Y.); (R.W.); (Z.Y.)
- China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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30
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Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biol 2022; 20:139. [PMID: 35698132 PMCID: PMC9195245 DOI: 10.1186/s12915-022-01342-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 05/30/2022] [Indexed: 12/25/2022] Open
Abstract
Background Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear. Results To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. Conclusions In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01342-y.
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Affiliation(s)
- Ke Cao
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| | - Zhen Peng
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Xing Zhao
- Novogene Bioinformatics Institute, Beijing, People's Republic of China
| | - Yong Li
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Kuozhan Liu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Pere Arus
- IRTA, Centre de Recerca en Agrigenòmica, CSIC-IRTA-UAB-UB, Campus UAB - Edifici CRAG, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Weichao Fang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Changwen Chen
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Xinwei Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Jinlong Wu
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Lirong Wang
- The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China. .,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
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Ullah U, Buttar ZA, Shalmani A, Muhammad I, Ud-Din A, Ali H. Genome-wide identification and expression analysis of CPP-like gene family in Triticum aestivum L. under different hormone and stress conditions. Open Life Sci 2022; 17:544-562. [PMID: 35647295 PMCID: PMC9123298 DOI: 10.1515/biol-2022-0051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/21/2022] Open
Abstract
The CPP-like plant‐specific transcription factor has a prominent role in plant development and growth through cell division and differential activities. However, little information is available about the CPP gene family in Triticum aestivum L. Herein, we identified 37 and 11 CPP genes in the wheat and rice genome databases, respectively. The phylogeny of the CPP protein-like family members was further divided into five subfamilies based on structural similarities and phenotypic functional diversities. The in silico expression analysis showed that CPP genes are highly expressed in some tissues, such as shoot apex, shoot, leaf, leaf sheath, and microspore. Furthermore, the qRT-PCR found higher expression for TaCPP gene family members in leaf, leaf blade, young spike, mature spike, and differential expression patterns under abiotic stresses, including heat, drought, salt, and hormonal treatment, such as indole acetic acid and 1-aminocyclopropane-1 carboxylic acid. We found that CPP gene family members are mostly located in the nucleus after infiltrating the CPP5-1B-GFP and TaCPP11-3B-GFP into tobacco leaves. The overexpression of the TaCPP5-1D gene revealed that the CPP gene positively regulates the germanium, shoot, and root activities in Arabidopsis. The TaCPP5-1D-overexpressed plants showed less anti-oxidative sensitivity under drought stress conditions. These results demonstrated that TaCPP5-1D protein has a crucial contribution by interacting with TaCPP11-3B protein in maintaining stress homeostasis under the natural and unfavorable environmental conditions for growth, development, and stress resistance activities. Therefore, this study could be used as pioneer knowledge to further investigate the function of CPP genes in plant growth and development.
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Affiliation(s)
- Uzair Ullah
- Department of Biotechnology and Genetic Engineering, University Mansehra, Dhodial, Pakistan
| | - Zeeshan Ali Buttar
- The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou, China
| | - Abdullah Shalmani
- College of Life Sciences, Northwest A & F University, Xianyang, China
| | - Izhar Muhammad
- College of Life Sciences, Northwest A & F University, Xianyang, China
| | - Aziz Ud-Din
- Department of Biotechnology and Genetic Engineering, University Mansehra, Dhodial, Pakistan
| | - Hamid Ali
- Department of Biotechnology and Genetic Engineering, University Mansehra, Dhodial, Pakistan
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Li M, Wang F, Ma J, Liu H, Ye H, Zhao P, Wang J. Comprehensive Evolutionary Analysis of CPP Genes in Brassica napus L. and Its Two Diploid Progenitors Revealing the Potential Molecular Basis of Allopolyploid Adaptive Advantage Under Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:873071. [PMID: 35548281 PMCID: PMC9085292 DOI: 10.3389/fpls.2022.873071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Allopolyploids exist widely in nature and have strong environmental adaptability. The typical allopolyploid Brassica napus L. is a widely cultivated crop, but whether it is superior to its diploid progenitors in abiotic stress resistance and the key genes that may be involved are not fully understood. Cystein-rich polycomb-like protein (CPP) genes encode critical transcription factors involved in the response of abiotic stress, including salt stress. To explore the potential molecular basis of allopolyploid adaptation to salt stress, we comprehensively analyzed the characteristics and salt stress response of the CPP genes in B. napus and its two diploid progenitors in this study. We found some molecular basis that might be associated with the adaptability of B. napus, including the expansion of the CPP gene family, the acquisition of introns by some BnCPPs, and abundant cis-acting elements upstream of BnCPPs. We found two duplication modes (whole genome duplication and transposed duplication) might be the main reasons for the expansion of CPP gene family in B. napus during allopolyploidization. CPP gene expression levels and several physiological indexes were changed in B. napus and its diploid progenitors after salt stress, suggesting that CPP genes might play important roles in the response of salt stress. We found that some BnCPPs might undergo new functionalization or subfunctionalization, and some BnCPPs also show biased expression, which might contribute to the adaptation of B. napus under saline environment. Compared with diploid progenitors, B. napus showed stronger physiological responses, and BnCPP gene expression also showed higher changes after salt stress, indicating that the allopolyploid B. napus had an adaptive advantage under salt stress. This study could provide evidence for the adaptability of polyploid and provide important clues for the study of the molecular mechanism of salt stress resistance in B. napus.
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Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Zinshteyn D, Barbash DA. Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster. PLoS Genet 2022; 18:e1010110. [PMID: 35324887 PMCID: PMC8982855 DOI: 10.1371/journal.pgen.1010110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 04/05/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022] Open
Abstract
Germline stem cells (GSCs) are the progenitor cells of the germline for the lifetime of an animal. In Drosophila, these cells reside in a cellular niche that is required for both their maintenance (self-renewal) and differentiation (asymmetric division resulting in a daughter cell that differs from the GSC). The stem cell—daughter cell transition is tightly regulated by a number of processes, including an array of proteins required for genome stability. The germline stem-cell maintenance factor Stonewall (Stwl) associates with heterochromatin, but its molecular function is poorly understood. We performed RNA-Seq on stwl mutant ovaries and found significant derepression of many transposon families but not heterochromatic genes. We also discovered inappropriate expression of multiple classes of genes. Most prominent are testis-enriched genes, including the male germline sex-determination switch Phf7, the differentiation factor bgcn, and a large testis-specific gene cluster on chromosome 2, all of which are upregulated or ectopically expressed in stwl mutant ovaries. Surprisingly, we also found that RNAi knockdown of stwl in somatic S2 cells results in ectopic expression of these testis genes. Using parallel ChIP-Seq and RNA-Seq experiments in S2 cells, we discovered that Stwl localizes upstream of transcription start sites and at heterochromatic sequences including repetitive sequences associated with telomeres. Stwl is also enriched at bgcn, suggesting that it directly regulates this essential differentiation factor. Finally, we identify Stwl binding motifs that are shared with known insulator binding proteins. We propose that Stwl affects gene regulation, including repression of male transcripts in the female germline, by binding insulators and establishing chromatin boundaries. Stem cells are defined by their ability to divide asymmetrically, resulting in a differentiated cell and a stem cell daughter. In fruit flies, sperm and egg production begins with germline stem cells (GSCs). The ability of a GSC to differentiate or self-renew is tightly regulated by a myriad of factors. Some of these are transcription factors, which are responsible for activating or suppressing other genes to promote one state in favor of another. Stonewall is an ovarian nuclear protein required for GSC self-renewal, whose molecular function is poorly understood. Here we show that Stonewall is responsible for preventing the activation of “male” molecular programming in the fruit fly ovary. When Stonewall is absent from the ovary, egg production is terminated and testis-specific genes become highly expressed, including the male transcript of Phf7, which induces male sexual identity in female germ cells. We also show that Stonewall is likely localizing to genomic insulators, which are regions of the genome that shield genes from nearby regulators. Our findings suggest that Stonewall helps to organize the genome in ovarian germ cells and prevent expression of male genes.
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Affiliation(s)
- Daniel Zinshteyn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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House MA, Young LW, Robinson SJ, Booker HM. Transcriptomic Analysis of Early Flowering Signals in ‘Royal’ Flax. PLANTS 2022; 11:plants11070860. [PMID: 35406840 PMCID: PMC9002848 DOI: 10.3390/plants11070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.
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Affiliation(s)
- Megan A. House
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Lester W. Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada;
| | - Helen M. Booker
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 56829)
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Kesawat MS, Kherawat BS, Singh A, Dey P, Routray S, Mohapatra C, Saha D, Ram C, Siddique KHM, Kumar A, Gupta R, Chung SM, Kumar M. Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:496. [PMID: 35214830 PMCID: PMC8880425 DOI: 10.3390/plants11040496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/19/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study's outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.
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Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, Rajasthan, India;
| | - Anupama Singh
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Prajjal Dey
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Snehasish Routray
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Chinmayee Mohapatra
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, Odisha, India;
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, Rajasthan, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ajay Kumar
- Agriculture Research Organization, Volcani Center, Department of Postharvest Science, Rishon Lezzion 50250, Israel;
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Korea;
| | - Sang-Min Chung
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
| | - Manu Kumar
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors. Int J Mol Sci 2022; 23:ijms23020614. [PMID: 35054810 PMCID: PMC8775908 DOI: 10.3390/ijms23020614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.
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Darragh K, Nelson DR, Ramírez SR. The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees. Genome Biol Evol 2021; 13:evab261. [PMID: 34850870 PMCID: PMC8670302 DOI: 10.1093/gbe/evab261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2021] [Indexed: 12/13/2022] Open
Abstract
The birth-and-death model of multigene family evolution describes how gene families evolve and diversify through duplication and deletion. The cytochrome P450s are one of the most diverse and well-studied multigene families, involved in both physiological and xenobiotic functions. Extensive studies of insect P450 genes have demonstrated their role in insecticide resistance. Bees are thought to experience toxin exposure through their diet of nectar and pollen, as well as the resin-collecting behavior exhibited by some species. Here, we describe the repertoire of P450 genes in the orchid bee Euglossa dilemma. Male orchid bees form perfume bouquets used in courtship displays by collecting volatile compounds, resulting in exposure to compounds known to be toxic. In addition, we conducted phylogenetic and selection analyses across ten bee species encompassing three bee families. We find that social behavior and resin collection are not correlated with the repertoire of P450 present in a bee species. However, our analyses revealed that P450 clades can be classified as stable and unstable, and that genes involved in xenobiotic metabolism are more likely to belong to unstable clades. Furthermore, we find that unstable clades are under more dynamic evolutionary pressures and exhibit signals of adaptive evolution. This work highlights the complexity of multigene family evolution, revealing that multiple factors contribute to the diversification, stability, and dynamics of this gene family. Furthermore, we provide a resource for future detailed studies investigating the function of different P450s in economically important bee species.
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Affiliation(s)
- Kathy Darragh
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - David R Nelson
- Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee, USA
| | - Santiago R Ramírez
- Department of Evolution and Ecology, University of California, Davis, California, USA
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Chai S, Huang X, Wu T, Xu S, Ren W, Yang G. Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. BMC Genomics 2021; 22:763. [PMID: 34702182 PMCID: PMC8547080 DOI: 10.1186/s12864-021-08084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. RESULTS In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. CONCLUSIONS Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the "cooling hypothesis", which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the "training hypothesis", which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.
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Affiliation(s)
- Simin Chai
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Xin Huang
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Tianzhen Wu
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shixia Xu
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Wenhua Ren
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Guang Yang
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development. Genes (Basel) 2021; 12:genes12101628. [PMID: 34681022 PMCID: PMC8535579 DOI: 10.3390/genes12101628] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/23/2022] Open
Abstract
Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.
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Wynen H, Heyland A. Hormonal Regulation of Programmed Cell Death in Sea Urchin Metamorphosis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.733787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Programmed cell death (PCD) has been identified as a key process in the metamorphic transition of indirectly developing organisms such as frogs and insects. Many marine invertebrate species with indirect development and biphasic life cycles face the challenge of completing the metamorphic transition of the larval body into a juvenile when they settle into the benthic habitat. Some key characteristics stand out during this transition in comparison to frogs and insects: (1) the transition is often remarkably fast and (2) the larval body is largely abandoned and few structures transition into the juvenile stage. In sea urchins, a group with a drastic and fast metamorphosis, development and destruction of the larval body is regulated by endocrine signals. Here we provide a brief review of the basic regulatory mechanisms of PCD in animals. We then narrow our discussion to metamorphosis with a specific emphasis on sea urchins with indirect life histories and discuss the function of thyroid hormones and histamine in larval development, metamorphosis and settlement of the sea urchin Strongylocentrotus purpuratus. We were able to annotate the large majority of PCD related genes in the sea urchin S. purpuratus and ongoing studies on sea urchin metamorphosis will shed light on the regulatory architecture underlying this dramatic life history transition. While we find overwhelming evidence for hormonal regulation of PCD in animals, especially in the context of metamorphosis, the mechanisms in many marine invertebrate groups with indirect life histories requires more work. Hence, we propose that studies of PCD in animals requires functional studies in whole organisms rather than isolated cells. We predict that future work, targeting a broader array of organisms will not only help to reveal important new functions of PCD but provide a fundamentally new perspective on its use in a diversity of taxonomic, developmental, and ecological contexts.
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Lažetić V, Troemel ER. Conservation lost: host-pathogen battles drive diversification and expansion of gene families. FEBS J 2021; 288:5289-5299. [PMID: 33190369 PMCID: PMC10901648 DOI: 10.1111/febs.15627] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022]
Abstract
One of the strongest drivers in evolution is the struggle to survive a host-pathogen battle. This pressure selects for diversity among the factors directly involved in this battle, including virulence factors deployed by pathogens, their corresponding host targets, and host immune factors. A logical outcome of this diversification is that over time, the sequence of many immune factors will not be evolutionarily conserved across a broad range of species. Thus, while universal sequence conservation is often hailed as the hallmark of the importance of a particular gene, the immune system does not necessarily play by these rules when defending against co-evolving pathogens. This loss of sequence conservation is in contrast to many signaling pathways in development and basic cell biology that are not targeted by pathogens. In addition to diversification, another consequence of host-pathogen battles can be an amplification in gene number, thus leading to large gene families that have sequence relatively specific to a particular strain, species, or clade. Here we highlight this general theme across a variety of pathogen virulence factors and host immune factors. We summarize the wide range and number across species of these expanded, lineage-specific host-pathogen factors including ubiquitin ligases, nucleotide-binding leucine-rich repeat receptors, GTPases, and proteins without obvious biochemical function but that nonetheless play key roles in immunity.
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Affiliation(s)
- Vladimir Lažetić
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Troemel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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Kesawat MS, Kherawat BS, Singh A, Dey P, Kabi M, Debnath D, Saha D, Khandual A, Rout S, Manorama, Ali A, Palem RR, Gupta R, Kadam AA, Kim HU, Chung SM, Kumar M. Genome-Wide Identification and Characterization of the Brassinazole-resistant ( BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:8743. [PMID: 34445448 PMCID: PMC8395832 DOI: 10.3390/ijms22168743] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.
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Affiliation(s)
- Mahipal Singh Kesawat
- Institute for Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul 08826, Korea;
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, India;
| | - Anupama Singh
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Prajjal Dey
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Mandakini Kabi
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Debanjana Debnath
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, India;
| | - Ansuman Khandual
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Sandeep Rout
- Faculty of Agriculture, Sri Sri University, Cuttack 754-006, India; (A.S.); (P.D.); (M.K.); (D.D.); (A.K.); (S.R.)
| | - Manorama
- Department of Dairy Microbiology, College of Dairy Science and Food Technology, Raipur 49200, India;
| | - Asjad Ali
- Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia;
| | - Ramasubba Reddy Palem
- Department of Medical Biotechnology, Biomedical Campus, Dongguk University, Seoul 10326, Korea;
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Avinash Ashok Kadam
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang 10326, Korea;
| | - Hyun-Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea;
| | - Sang-Min Chung
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
| | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
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Genome-wide survey of sugar beet (Beta vulgaris subsp. vulgaris) Dof transcription factors reveals structural diversity, evolutionary expansion and involvement in taproot development and biotic stress response. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00777-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L. Int J Mol Sci 2021; 22:ijms22147396. [PMID: 34299014 PMCID: PMC8303626 DOI: 10.3390/ijms22147396] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022] Open
Abstract
PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.
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Ma L, Dong C, Song C, Wang X, Zheng X, Niu Y, Chen S, Feng W. De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. Comput Struct Biotechnol J 2021; 19:3954-3963. [PMID: 34377362 PMCID: PMC8318827 DOI: 10.1016/j.csbj.2021.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
Rehmannia glutinosa is a potent medicinal plant with a significant importance in traditional Chinese medicine. Its root is enriched with various bioactive molecules mainly iridoids, possessing important pharmaceutical properties. However, the molecular biology and evolution of R. glutinosa have been largely unexplored. Here, we report a reference genome of R. glutinosa using Nanopore technology, Illumina and Hi-C sequencing. The assembly genome is 2.49 Gb long with a scaffold N50 length of 70 Mb and high heterozygosity (2%). Since R. glutinosa is an autotetraploid (4n = 56), the difference between each set of chromosomes is very small, and it is difficult to distinguish the two sets of chromosomes using Hi-C. Hence, only one set of the genome size was mounted to the chromosome level. Scaffolds covering 52.61% of the assembled genome were anchored on 14 pseudochromosomes. Over 67% of the genome consists of repetitive sequences dominated by Copia long terminal repeats and 48,475 protein-coding genes were predicted. Phylogenetic analysis corroborates the placement of R. glutinosa in the Orobanchaceae family. Our results indicated an independent and very recent whole genome duplication event that occurred 3.64 million year ago in the R. glutinosa lineage. Comparative genomics analysis demonstrated expansion of the UDP-dependent glycosyltransferases and terpene synthase gene families, known to be involved in terpenoid biosynthesis and diversification. Furthermore, the molecular biosynthetic pathway of iridoids has been clarified in this work. Collectively, the generated reference genome of R. glutinosa will facilitate discovery and development of important pharmacological compounds.
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Affiliation(s)
- Ligang Ma
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chengming Dong
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chi Song
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaolan Wang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
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Lassance JM, Ding BJ, Löfstedt C. Evolution of the codling moth pheromone via an ancient gene duplication. BMC Biol 2021; 19:83. [PMID: 33892710 PMCID: PMC8063362 DOI: 10.1186/s12915-021-01001-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/07/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Defining the origin of genetic novelty is central to our understanding of the evolution of novel traits. Diversification among fatty acid desaturase (FAD) genes has played a fundamental role in the introduction of structural variation in fatty acyl derivatives. Because of its central role in generating diversity in insect semiochemicals, the FAD gene family has become a model to study how gene family expansions can contribute to the evolution of lineage-specific innovations. Here we used the codling moth (Cydia pomonella) as a study system to decipher the proximate mechanism underlying the production of the ∆8∆10 signature structure of olethreutine moths. Biosynthesis of the codling moth sex pheromone, (E8,E10)-dodecadienol (codlemone), involves two consecutive desaturation steps, the first of which is unusual in that it generates an E9 unsaturation. The second step is also atypical: it generates a conjugated diene system from the E9 monoene C12 intermediate via 1,4-desaturation. RESULTS Here we describe the characterization of the FAD gene acting in codlemone biosynthesis. We identify 27 FAD genes corresponding to the various functional classes identified in insects and Lepidoptera. These genes are distributed across the C. pomonella genome in tandem arrays or isolated genes, indicating that the FAD repertoire consists of both ancient and recent duplications and expansions. Using transcriptomics, we show large divergence in expression domains: some genes appear ubiquitously expressed across tissue and developmental stages; others appear more restricted in their expression pattern. Functional assays using heterologous expression systems reveal that one gene, Cpo_CPRQ, which is prominently and exclusively expressed in the female pheromone gland, encodes an FAD that possesses both E9 and ∆8∆10 desaturation activities. Phylogenetically, Cpo_CPRQ clusters within the Lepidoptera-specific ∆10/∆11 clade of FADs, a classic reservoir of unusual desaturase activities in moths. CONCLUSIONS Our integrative approach shows that the evolution of the signature pheromone structure of olethreutine moths relied on a gene belonging to an ancient gene expansion. Members of other expanded FAD subfamilies do not appear to play a role in chemical communication. This advises for caution when postulating the consequences of lineage-specific expansions based on genomics alone.
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Affiliation(s)
- Jean-Marc Lassance
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Bao-Jian Ding
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Christer Löfstedt
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden.
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Lee DY, Jeon J, Kim KT, Cheong K, Song H, Choi G, Ko J, Opiyo SO, Correll JC, Zuo S, Madhav S, Wang GL, Lee YH. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 2021; 22:242. [PMID: 33827423 PMCID: PMC8028249 DOI: 10.1186/s12864-021-07549-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07549-7.
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Affiliation(s)
- Da-Young Lee
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, 57922, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Jaeho Ko
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Stephen O Opiyo
- Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus, The Ohio State University, Columbus, OH, 43210, USA
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AK, 72701, USA
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Sheshu Madhav
- Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, 500030, Telangana, India
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea. .,Center for Fungal Genetic Resources, Plant Immunity Research Center, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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Wei X, Li J, Xiao J, Huang D. Gene duplication and subsequent functional diversification of maltase in fig wasp (Chalcidoidea, Hymenoptera). Int J Biol Macromol 2021; 182:482-491. [PMID: 33838190 DOI: 10.1016/j.ijbiomac.2021.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Maltase can catalyze the hydrolysis of α-1,4-glucosidic linkages and release α-d-glucoses that are used as a source of energy by insects. Maltase has been extensively studied in Lepidoptera and Diptera, while the characterization and evolutionary history of maltase are largely unknown in Hymenoptera. Here, we undertook a bioinformatics study and identified 105 maltase genes in 12 fig wasp species. Together with the maltase genes of Nasonia vitripennis and Apis mellifera, phylogenetic analysis showed that all the maltase genes were clustered into three clades. Clade I and III included maltase genes from all the fig wasp species, while clade II contained the maltase genes from non-pollinating fig wasps (NPFWs) only. Interestingly, the maltase genes located in clade II were intronless. Fig pollinators and NPFWs had lineage-specific gene expansion in clade I and II respectively, which were mainly derived from tandem duplications. The three clades displayed distinct gene structures. Furthermore, maltase showed significant functional divergence among the three clades and the critical amino acid sites were detected. These sites could be responsible for the ligand-binding preference and hydrolytic specificity. Overall, our results demonstrated that maltase might contribute to the discrepancy of life histories and feeding regimes between fig pollinators and NPFWs.
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Affiliation(s)
- Xianqin Wei
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiaxing Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jinhua Xiao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Dawei Huang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Glover ML, Burroughs AM, Monem PC, Egelhofer TA, Pule MN, Aravind L, Arribere JA. NONU-1 Encodes a Conserved Endonuclease Required for mRNA Translation Surveillance. Cell Rep 2021; 30:4321-4331.e4. [PMID: 32234470 DOI: 10.1016/j.celrep.2020.03.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 01/31/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
Cellular translation surveillance rescues ribosomes that stall on problematic mRNAs. During translation surveillance, endonucleolytic cleavage of the problematic mRNA is a critical step in rescuing stalled ribosomes. Here we identify NONU-1 as a factor required for translation surveillance pathways including no-go and nonstop mRNA decay. We show that (1) NONU-1 reduces nonstop and no-go mRNA levels; (2) NONU-1 contains an Smr RNase domain required for mRNA decay; (3) the domain architecture and catalytic residues of NONU-1 are conserved throughout metazoans and eukaryotes, respectively; and (4) NONU-1 is required for the formation of mRNA cleavage fragments in the vicinity of stalled ribosomes. We extend our results in C. elegans to homologous factors in S. cerevisiae, showing the evolutionarily conserved function of NONU-1. Our work establishes the identity of a factor critical to translation surveillance and will inform mechanistic studies at the intersection of translation and mRNA decay.
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Affiliation(s)
- Marissa L Glover
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - A Max Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Parissa C Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Thea A Egelhofer
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Makena N Pule
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Joshua A Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.
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50
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Chen H, Lu Q, Chen X, Ling X, Liu P, Liu N, Wang W, Zhang J, Qi Q, Ding W, Zhang X, Feng Y, Zhang Y, Chen MS, King-Jones K. Genome assembly and methylome analysis of the white wax scale insect provides insight into sexual differentiation of metamorphosis in hexapods. Mol Ecol Resour 2021; 21:1983-1995. [PMID: 33709555 DOI: 10.1111/1755-0998.13376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Scale insects are hemimetabolous, showing "incomplete" metamorphosis and no true pupal stage. Ericerus pela, commonly known as the white wax scale insect (hereafter, WWS), is a wax-producing insect found in Asia and Europe. WWS displays dramatic sexual dimorphism, with notably different metamorphic fates in males and females. Males develop into winged adults, while females are neotenic and maintain a nymph-like appearance, which are flightless and remain stationary. Here, we report the de novo assembly of the WWS genome with a size of 638.30 Mbp (69.68 Mbp for scaffold N50) by PacBio sequencing and Hi-C. These data allowed us to perform a robust phylogenetic analysis comprising 24,923 gene orthogroups from 16 representative insect genomes. This analysis indicated that holometabola evolved from insects with incomplete metamorphosis in the Late Carboniferous, about 50 million years earlier than previously thought. To study the distinct developmental fates of males and females, we analysed the methylome landscape in either sex. Surprisingly, WWS displayed high methylation levels (4.42% for males) when compared to other insects. We observed differential methylation patterns in males and females for genes involved in steroid and sesquiterpenoid production as well as genes acting in fatty acid metabolism pathways. We measured titre profiles for ecdysone, the principal insect steroid hormone, and juvenile hormone (a sesquiterpenoid) in both males and females, which suggested that these hormones are the primary drivers of sexually dimorphic development. Our results provide a comprehensive genomic and epigenomic resource of scale insects that provide new insights into the evolution of metamorphosis and sexual dimorphism in insects.
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Affiliation(s)
- Hang Chen
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China.,The Key Laboratory of Cultivating and Utilization of Resources Insects, State Forestry Administration, Kunming, China
| | - Qin Lu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Xiaoming Chen
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China.,The Key Laboratory of Cultivating and Utilization of Resources Insects, State Forestry Administration, Kunming, China
| | - Xiaofei Ling
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Pengfei Liu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Ni Liu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Weiwei Wang
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Jinwen Zhang
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Qian Qi
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Weifeng Ding
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Xin Zhang
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | - Ying Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
| | | | - Ming-Shun Chen
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - Kirst King-Jones
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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