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Molecular Evolutionary and Comparative Genomics Analyses in Plants
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Molecular Evolutionary and Comparative Genomics Analyses in Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2021) | Viewed by 17437

Special Issue Editors

Dr. Elizabeth R. Waters

E-Mail Website
Guest Editor
Department of Biology, San Diego State University, San Diego, CA, USA
Interests: functional evolution of proteins; gene family evolution; plant thermotolerance
Dr. Tanya Renner

E-Mail Website
Guest Editor
Department of Entomology, The Pennsylvania State University, 520 ASI Building, University Park, PA 16802, USA
Interests: molecular evolution; genomics; biochemistry; physiology; morphology

Special Issue Information

Dear Colleagues,  

It has been only twenty years since the publication of the first complete plant genome, that of Arabidopsis thaliana. In the ten years following this monumental task, the number of well-curated new plant genomes was in the single digits. Now, the number of plant genomes available for study increases daily and is in the hundreds. What have we learned in the last ten years? What new questions are we able to ask with this exciting wealth of data? The focus of this Special Issue will be on where plant evolutionary and comparative genomics is going for the next ten years. Of particular interest are papers that address questions of genomic organization from an evolutionary perspective and that examine the genomes of basal plants as well as angiosperms. Polyploidy and whole genome duplication (WGD) are common within plants, and these events have shaped plant genomes and plant gene families. Submission of manuscripts that describe studies that examine the impacts of both recent and ancient WGD events and the processes of diploidization are encouraged. Population-level studies of genome level variation have informed our understanding of local adaptation and provided needed information on fine-scale evolutionary processes. Manuscripts that focus on comparative genomic studies within species or among closely related species are also encouraged.

Dr. Elizabeth R. Waters
Dr. Tanya Renner
Guest Editors

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Keywords

  • plant evolutionary genomics
  • plant genome evolution
  • whole genome duplication
  • diploidization
  • lineage-specific expansions
  • gene family evolution

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Published Papers (4 papers)

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Research

18 pages, 2956 KiB  
Article
Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase
by Zequn Chen, Kelly J. Vining, Xiwu Qi, Xu Yu, Ying Zheng, Zhiqi Liu, Hailing Fang, Li Li, Yang Bai, Chengyuan Liang, Weilin Li and Bernd Markus Lange
Genes 2021, 12(4), 518; https://doi.org/10.3390/genes12040518 - 2 Apr 2021
Cited by 27 | Viewed by 4858 | Correction
Abstract
Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there [...] Read more.
Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha. Full article
(This article belongs to the Special Issue Molecular Evolutionary and Comparative Genomics Analyses in Plants)
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19 pages, 2950 KiB  
Article
Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis
by Panqiao Wang, Xiaqing Yu, Zaobing Zhu, Yufei Zhai, Qinzheng Zhao, Ya Meng, Ji Li, Qunfeng Lou and Jinfeng Chen
Genes 2020, 11(12), 1500; https://doi.org/10.3390/genes11121500 - 12 Dec 2020
Cited by 6 | Viewed by 2903
Abstract
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S14 [...] Read more.
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S14), its diploid parents, and the F1 hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in C. hytivus, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S14, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution. Full article
(This article belongs to the Special Issue Molecular Evolutionary and Comparative Genomics Analyses in Plants)
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23 pages, 2149 KiB  
Article
Gene Loss and Evolution of the Plastome
by Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Adil Khan, Abeer Hashem, Elsayed Fathi Abd_Allah and Ahmed Al-Harrasi
Genes 2020, 11(10), 1133; https://doi.org/10.3390/genes11101133 - 25 Sep 2020
Cited by 51 | Viewed by 5471
Abstract
Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the [...] Read more.
Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages. Full article
(This article belongs to the Special Issue Molecular Evolutionary and Comparative Genomics Analyses in Plants)
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11 pages, 2419 KiB  
Article
Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)
by Delil A. Chincoya, Alejandro Sanchez-Flores, Karel Estrada, Clara E. Díaz-Velásquez, Antonio González-Rodríguez, Felipe Vaca-Paniagua, Patricia Dávila, Salvador Arias and Sofía Solórzano
Genes 2020, 11(7), 830; https://doi.org/10.3390/genes11070830 - 21 Jul 2020
Cited by 9 | Viewed by 3259
Abstract
In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared [...] Read more.
In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies. Full article
(This article belongs to the Special Issue Molecular Evolutionary and Comparative Genomics Analyses in Plants)
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