1
|
Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [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: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
Collapse
Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
2
|
Wang H, Zhang Y, Zhang L, Wang J, Guo H, Zong J, Chen J, Li D, Li L, Liu J, Li J. Molecular Characterization and Phylogenetic Analysis of Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence. Curr Issues Mol Biol 2024; 46:1635-1650. [PMID: 38392224 PMCID: PMC10888139 DOI: 10.3390/cimb46020106] [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: 01/08/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.
Collapse
Affiliation(s)
- Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| |
Collapse
|
3
|
Liu LJ, Liu CK, Cai J, Deng JJ, He XJ, Zhou SD. The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis. BMC PLANT BIOLOGY 2024; 24:106. [PMID: 38342898 PMCID: PMC10860227 DOI: 10.1186/s12870-024-04784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia. Despite many previous taxonomic insights into it, phylogenetic studies of the genus are still lacking. And the establishment of a robust phylogenetic framework remains elusive, impeding advancements and revisions in the taxonomic system for this genus. Plastomes with greater variability in their genetic characteristics hold promise for building a more robust Libanotis phylogeny. RESULTS During our research, we sequenced, assembled, and annotated complete plastomes for twelve Libanotis species belong to three sections and two closely related taxa. We conducted a comprehensive comparative analysis through totally thirteen Libanotis plastomes for the genus, including an additional plastome that had been published. Our results suggested that Libanotis plastome was highly conserved between different subclades, while the coding regions were more conserved than the non-coding regions, and the IR regions were more conserved than the single copy regions. Nevertheless, eight mutation hotspot regions were identified among plastomes, which can be considered as candidate DNA barcodes for accurate species identification in Libanotis. The phylogenetic analyses generated a robustly framework for Libanotis and revealed that Libanotis was not a monophyletic group and their all three sections were polygenetic. Libanotis schrenkiana was sister to L. sibirica, type species of this genus, but the remainders scattered within Selineae. CONCLUSION The plastomes of Libanotis exhibited a high degree of conservation and was effective in enhancing the support and resolution of phylogenetic analyses within this genus. Based on evidence from both phylogeny and morphology, we propose the recognition of "Libanotis sensu stricto" and provide taxonomic recommendations for other taxa that previously belonged to Libanotis. In conclusion, our study not only revealed the phylogenetic position and plastid evolution of Libanotis, but also provided new insights into the phylogeny of the family Apiaceae and phylogenetic relationships within the tribe Selineae.
Collapse
Affiliation(s)
- Li-Jia Liu
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- College of Resources Environment and Chemistry, Chuxiong Normal University, Chuxiong, 675000, China
| | - Jing Cai
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jiao-Jiao Deng
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Song-Dong Zhou
- Key Laboratory of Bio‑Resources and Eco‑Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
4
|
Javaid N, Ramzan M, Jabeen S, Shah MN, Danish S, Hirad AH. Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan. BMC PLANT BIOLOGY 2023; 23:658. [PMID: 38124056 PMCID: PMC10731703 DOI: 10.1186/s12870-023-04670-5] [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: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides. RESULTS The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ. CONCLUSION The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.
Collapse
Affiliation(s)
- Nida Javaid
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan.
| | - Shagufta Jabeen
- Government Associate College for Women Ahmedpur East, Bahawalpur, Punjab, Pakistan
| | - Muhammad Nadeem Shah
- Department of Agriculture, Government College University Lahore, Lahore, Punjab, Pakistan
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, Florida, USA
| | - Subhan Danish
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box.2455, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
5
|
Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
Collapse
Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
| |
Collapse
|
6
|
Rakotonasolo RA, Dransfield S, Haevermans T, Ralimanana H, Vorontsova MS, Zhou MY, Li DZ. New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes. PLANT DIVERSITY 2023; 45:125-132. [PMID: 37069926 PMCID: PMC10105074 DOI: 10.1016/j.pld.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 06/19/2023]
Abstract
The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae from herbarium specimens is even more so. Molecular phylogenetic work is critical to understanding this group of bamboos. Here, comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures. We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions. Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which is paraphyletic and forms two distant clades. The type species of Nastus (Clade II) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar (Clade VI). Clade VI (Malagasy Nastus) is sister to the Sokinochloa + Hitchcockella clade (Clade V), and both clades have a clumping habit with short-necked pachymorph rhizomes. The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade IV. Clade III, which has the highest generic diversity, consists of Cathariostachys, Perrierbambus, Sirochloa, and Valiha, which are also morphologically diverse. This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae, an understudied subtribe of bamboo.
Collapse
Affiliation(s)
- Rivontsoa A. Rakotonasolo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Department Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, 101, Madagascar
- Kew Madagascar Conservation Center, Antananarivo, 101, Madagascar
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Soejatmi Dransfield
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Thomas Haevermans
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de La Recherche Scientifique, École Pratique des Hautes Études, Université des Antilles, Sorbonne Université, 45 Rue Buffon, CP 50, 75005, Paris, France
| | | | - Maria S. Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
7
|
Hu Y, Sun Y, Zhu QH, Fan L, Li J. Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. Curr Genomics 2023; 23:369-384. [PMID: 37920556 PMCID: PMC10173419 DOI: 10.2174/1389202924666221201140603] [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: 05/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 12/11/2022] Open
Abstract
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
Collapse
Affiliation(s)
- Yiyu Hu
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
8
|
Delfini C, Aliscioni SS, Acosta JM, Pensiero JF, Zuloaga FO. An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L. PLANTS (BASEL, SWITZERLAND) 2023; 12:749. [PMID: 36840098 PMCID: PMC9966601 DOI: 10.3390/plants12040749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Subtribe Cenchrinae, so-called as the "bristle clade", is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an "incertae sedis" species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.
Collapse
Affiliation(s)
- Carolina Delfini
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - Sandra S. Aliscioni
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Juan M. Acosta
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - José F. Pensiero
- Instituto de Ciencias Agropecuarias del Litoral, UNL–CONICET–FCA, Kreder 2805, Esperanza 3080HOF, Santa Fe, Argentina
| | - Fernando O. Zuloaga
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| |
Collapse
|
9
|
Wang R, Zhang XJ, Guo XX, Xing Y, Qu XJ, Fan SJ. Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1002724. [PMID: 36407581 PMCID: PMC9666777 DOI: 10.3389/fpls.2022.1002724] [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: 07/25/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae. Simultaneously, nine monophyletic lineages were revealed in Cynodonteae: supersubtribe Boutelouodinae, subtribes Tripogoninae, Aeluropodinae, Eleusininae, Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. Within the tribe of Cynodonteae, the basal lineage is supersubtribe Boutelouodinae and Tripogoninae is sister to the remaining lineages. The clade formed of Aeluropodinae and Eleusininae is sister to the clade composed of Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. The clade comprising Dactylocteniinae and supersubtribe Gouiniodinae is sister to the clade comprising Cleistogenes, Orinus, and Triodiinae. Acrachne is a genus within Eleusininae but not within Dactylocteniinae. Molecular evidence determined that Diplachne is not clustered with Leptochloa, which indicated that Diplachne should not be combined into Leptochloa. Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas the recently proposed subtribe Orininae was not supported. Cynodonteae was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving its phylogenetic relationships. Ancestral state reconstructions of morphological characters showed that the most recent common ancestor (MRCA) of Chloridoideae has a panicle, multiple florets in each spikelet, the peaked type of stomatal subsidiary cells, and a saddle-shaped phytoliths, while the ancestral morphological characters of Cynodonteae are the panicle, peaked type of stomatal subsidiary cells, sharp-cap cell typed and equal-base-cell microhair, and square-shaped phytoliths. Overall, plastome phylogenomics provides new insights into the phylogenetic relationships and morphological character evolution of Chloridoideae.
Collapse
Affiliation(s)
- Rong Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiu-Xiu Guo
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yan Xing
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| |
Collapse
|
10
|
Nasiri A, Kazempour-Osaloo S, Hamzehee B, Bull RD, Saarela JM. A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus. PeerJ 2022; 10:e13884. [PMID: 36193423 PMCID: PMC9526414 DOI: 10.7717/peerj.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnLUAG , matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea-B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus.
Collapse
Affiliation(s)
- Akram Nasiri
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran,Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Hamzehee
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Roger D. Bull
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| |
Collapse
|
11
|
Xie P, Liu J, Lu R, Zhang Y, Sun X. Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza. Front Genet 2022; 13:991900. [PMID: 36147495 PMCID: PMC9486079 DOI: 10.3389/fgene.2022.991900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/10/2022] [Indexed: 11/15/2022] Open
Abstract
The exploitation of plant disease resistance (R) genes in breeding programs is an effective strategy for coping with pathogens. An understanding of R gene variation is the basis for this strategy. Rice blast disease, caused by the Magnaporthe oryzae fungus, is a destructive disease of rice. The rice blast resistance gene Pi-d2 represents a new class of plant R gene because of its novel extracellular domain. We investigated the nucleotide polymorphism, phylogenetic topology and evolution patterns of the Pi-d2 gene among 67 cultivated and wild rice relatives. The Pi-d2 gene originated early in the basal Poales and has remained as a single gene without expansion. The striking finding is that susceptible Pi-d2 alleles might be derived from a single nucleotide substitution of the resistant alleles after the split of Oryza subspecies. Functional pleiotropy and linkage effects are proposed for the evolution and retention of the disease-susceptible alleles in rice populations. One set of DNA primers was developed from the polymorphic position to detect the functional nucleotide polymorphism for disease resistance of the Pi-d2 gene based on conventional Polymerase Chain Reaction. The nucleotide diversity level varied between different domains of the Pi-d2 gene, which might be related to distinct functions of each domain in the disease defense response. Directional (or purifying) selection appears dominant in the molecular evolution of the Pi-d2 gene and has shaped its conserved variation pattern.
Collapse
Affiliation(s)
| | | | | | | | - Xiaoqin Sun
- *Correspondence: Yanmei Zhang, ; Xiaoqin Sun,
| |
Collapse
|
12
|
Petersen KB, Kellogg EA. Diverse ecological functions and the convergent evolution of grass awns. AMERICAN JOURNAL OF BOTANY 2022; 109:1331-1345. [PMID: 36048829 PMCID: PMC9828495 DOI: 10.1002/ajb2.16060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The awn of grasses is a long, conspicuous outgrowth of the floral bracts in a grass spikelet. It is known to impact agricultural yield, but we know little about its broader ecological function, nor the selective forces that lead to its evolution. Grass awns are phenotypically diverse across the extant ~12,000 species of Poaceae. Awns have been lost and gained repeatedly over evolutionary time, between and within lineages, suggesting that they could be under selection and might provide adaptive benefit in some environments. Despite the phylogenetic context, we know of no studies that have tested whether the origin of awns correlates with putative selective forces on their form and function. Presence or absence of awns is not plastic; rather, heritability is high. The awns of grasses often are suggested as adaptations for dispersal, and most experimental work has been aimed at testing this hypothesis. Proposed dispersal functions include soil burial, epizoochory, and aerial orientation. Awns may also protect the seed from drought, herbivores, or fire by helping it become buried in soil. We do not fully understand the fitness or nutrient costs of awn production, but in some species awns function in photosynthesis, providing carbon to the seed. Here we show that awns likely provide an adaptive advantage, but argue that studies on awn function have lacked critical phylogenetic information to demonstrate adaptive convergent evolution, are taxonomically biased, and often lack clear alternative hypotheses.
Collapse
|
13
|
Sokoloff DD, Fomichev CI, Rudall PJ, Macfarlane TD, Remizowa MV. Evolutionary history of the grass gynoecium. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4637-4661. [PMID: 35512454 DOI: 10.1093/jxb/erac182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
The grass family (Poaceae) includes cereal crops that provide a key food source for the human population. The food industry uses the starch deposited in the cereal grain, which develops directly from the gynoecium. Morphological interpretation of the grass gynoecium remains controversial. We re-examine earlier hypotheses and studies of morphology and development in the context of more recent analyses of grass phylogenetics and developmental genetics. Taken in isolation, data on gynoecium development in bistigmatic grasses do not contradict its interpretation as a solitary ascidiate carpel. Nevertheless, in the context of other data, this interpretation is untenable. Broad comparative analysis in a modern phylogenetic context clearly demonstrates that the grass gynoecium is pseudomonomerous. A bistigmatic grass gynoecium has two sterile carpels, each producing a stigma, and a fertile carpel that lacks a stigma. To date, studies of grass developmental genetics and developmental morphology have failed to fully demonstrate the composite nature of the grass gynoecium be-cause its complex evolutionary history is hidden by extreme organ integration. It is problematic to interpret the gynoecium of grasses in terms of normal angiosperm gynoecium typology. Even the concept of a carpel becomes misleading in grasses; instead, we recommend the term pistil for descriptive purposes.
Collapse
Affiliation(s)
- Dmitry D Sokoloff
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
| | - Constantin I Fomichev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Terry D Macfarlane
- Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre WA 6983, Australia
| | - Margarita V Remizowa
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
| |
Collapse
|
14
|
Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M. Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense. FRONTIERS IN PLANT SCIENCE 2022; 13:779830. [PMID: 35874012 PMCID: PMC9296850 DOI: 10.3389/fpls.2022.779830] [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: 09/19/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.
Collapse
Affiliation(s)
- Eka Giorgashvili
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Katja Reichel
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Calvinna Caswara
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Vuqar Kerimov
- Institute of Botany, Azerbaijan National Academy of Sciences (ANAS), Baku, Azerbaijan
| | - Thomas Borsch
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Michael Gruenstaeudl
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
15
|
Kellogg EA. Genetic control of branching patterns in grass inflorescences. THE PLANT CELL 2022; 34:2518-2533. [PMID: 35258600 PMCID: PMC9252490 DOI: 10.1093/plcell/koac080] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.
Collapse
|
16
|
Hyeon Jeong J, Joo Jung W, Weon Seo Y. Genome-wide identification and expression analysis of the annexin gene family in rye (Secale cereale L.). Gene 2022; 838:146704. [PMID: 35772654 DOI: 10.1016/j.gene.2022.146704] [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: 02/27/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022]
Abstract
Rye (Secale cereale L.) is one of the major cereal crops belonging to the family Triticeae and is known to be most tolerant to diverse abiotic stresses, such as cold, heat, osmotic, and salt stress. With the advancements in sequencing and bioinformatics technologies, the sequence information for the large and repetitive rye genome has become available. Plant annexins are components of the calcium signaling network that regulate signaling in abiotic stress tolerance via Ca2+ transport. In this study, we identified 12 novel rye annexin gene families by investigating the recently published rye genome. The annexin gene families were classified into five groups according to phylogenetic conserved motif analyses. Cis-element analysis revealed that these genes may be regulated by light, ABA, MeJA, and MYB transcription factors. Chromosome localization of the genes revealed that the gene family was conserved in many species, and high synteny was observed between the rye and wheat annexin genes. Plant tissue-specific gene expression revealed that rye annexin genes are mostly expressed in the roots, and gene expression analysis under cold, heat, PEG, and NaCl treatments showed that the genes were differentially expressed in response to different types of stresses, suggesting that each gene has a distinct role in stress signaling. The findings of this study provide a basis for further research on the role of rye annexin genes in abiotic stress signaling.
Collapse
Affiliation(s)
- Ji Hyeon Jeong
- Department of Plant Biotechnology, Korea University, Seoul 02841, South Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, South Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul 02841, South Korea.
| |
Collapse
|
17
|
The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated. Proc Natl Acad Sci U S A 2022; 119:e2112737119. [PMID: 35617436 DOI: 10.1073/pnas.2112737119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceResilience is required to withstand or mitigate the effect of human-induced climate change. Today whole ecosystems are affected by climate change, but our understanding of their evolution and natural response is limited, often restricted to individual populations or species. The enigmatic flora on the tops of the African sky islands is isolated and unique, showing striking adaptations to the harsh tropical alpine conditions. Here we analyze genome data from a large fraction of afroalpine plants and show that this remarkable flora has a dynamic history with frequent colonizations and extinctions, most likely caused by previous natural climate changes during the ice-age cycles. The flora will be particularly vulnerable to human-induced climate warming, reducing alpine habitat into successively smaller areas.
Collapse
|
18
|
Wu D, Jiang B, Ye CY, Timko MP, Fan L. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. PLANT COMMUNICATIONS 2022; 3:100320. [PMID: 35576160 PMCID: PMC9251436 DOI: 10.1016/j.xplc.2022.100320] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 05/11/2023]
Abstract
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.
Collapse
Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
19
|
Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
Collapse
Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
| |
Collapse
|
20
|
Bianconi ME, Christin PA, Dunning LT. Inferring the genome-wide history of grasses. MOLECULAR PLANT 2022; 15:591-592. [PMID: 35307592 DOI: 10.1016/j.molp.2022.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
21
|
Gagnon E, Hilgenhof R, Orejuela A, McDonnell A, Sablok G, Aubriot X, Giacomin L, Gouvêa Y, Bragionis T, Stehmann JR, Bohs L, Dodsworth S, Martine C, Poczai P, Knapp S, Särkinen T. Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum. AMERICAN JOURNAL OF BOTANY 2022; 109:580-601. [PMID: 35170754 PMCID: PMC9321964 DOI: 10.1002/ajb2.1827] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/14/2021] [Indexed: 05/13/2023]
Abstract
PREMISE Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. METHODS A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). RESULTS While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. CONCLUSIONS We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.
Collapse
Affiliation(s)
- Edeline Gagnon
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Rebecca Hilgenhof
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Angela McDonnell
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden, 1000 Lake Cook RdGlencoeIllinois60022USA
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit)University of HelsinkiPO Box 7 FI‐00014HelsinkiFinland
- Organismal and Evolutionary Biology Research Programme (OEB)Viikki Plant Science Centre (ViPS)PO Box 65, FI‐00014 University of HelsinkiFinland
| | - Xavier Aubriot
- Université Paris‐Saclay, CNRS, AgroParisTech, ÉcologieSystématique et ÉvolutionOrsay91405France
| | - Leandro Giacomin
- Instituto de Ciências e Tecnologia das Águas & Herbário HSTMUniversidade Federal do Oeste do Pará, Rua Vera Paz, sn, Santarém, CEP 68040‐255PABrazil
| | - Yuri Gouvêa
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - Thamyris Bragionis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - João Renato Stehmann
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - Lynn Bohs
- Department of BiologyUniversity of UtahSalt Lake CityUtah84112USA
| | - Steven Dodsworth
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonLU1 3JUUK
- Royal Botanic Gardens, Kew, RichmondSurreyTW9 3AEUK
| | | | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit)University of HelsinkiPO Box 7 FI‐00014HelsinkiFinland
- Faculity of Environmental and Biological SciencesUniversity of HelsinkiFI‐00014Finland
| | - Sandra Knapp
- Department of Life SciencesNatural History MuseumCromwell RoadLondonSW7 5BDUK
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
| |
Collapse
|
22
|
Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera. FORESTS 2022. [DOI: 10.3390/f13020280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.
Collapse
|
23
|
Han Y, Gao Y, Li Y, Zhai X, Zhou H, Ding Q, Ma L. Chloroplast Genes Are Involved in The Male-Sterility of K-Type CMS in Wheat. Genes (Basel) 2022; 13:genes13020310. [PMID: 35205355 PMCID: PMC8871828 DOI: 10.3390/genes13020310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.
Collapse
Affiliation(s)
- Yucui Han
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yujie Gao
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yun Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
| | - Xiaoguang Zhai
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (Q.D.); (L.M.)
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
- Correspondence: (Q.D.); (L.M.)
| |
Collapse
|
24
|
Epichloë scottii sp. nov., a new endophyte isolated from Melica uniflora is the missing ancestor of Epichloë disjuncta. IMA Fungus 2022; 13:2. [PMID: 35109929 PMCID: PMC8812020 DOI: 10.1186/s43008-022-00088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Here we describe a new, haploid and stroma forming species within the genus Epichloë, as Epichloë scottii sp. nov. The fungus was isolated from Melica uniflora growing in Bad Harzburg, Germany. Phylogenetic reconstruction using a combined dataset of the tubB and tefA genes strongly support that E. scottii is a distinct species and the so far unknown ancestor species of the hybrid E. disjuncta. A distribution analysis showed a high infection rate in close vicinity of the initial sampling site and only two more spots with low infection rates. Genetic variations in key genes required for alkaloid production suggested that E. scottii sp. nov. might not be capable of producing any of the major alkaloids including ergot alkaloid, loline, indole-diterpene and peramine. All isolates and individuals found in the distribution analysis were identified as mating-type B explaining the lack of mature stromata during this study. We further release a telomere-to-telomere de novo assembly of all seven chromosomes and the mitogenome of E. scottii sp. nov.
Collapse
|
25
|
Zhang L, Zhu X, Zhao Y, Guo J, Zhang T, Huang W, Huang J, Hu Y, Huang CH, Ma H. Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. Mol Biol Evol 2022; 39:6521033. [PMID: 35134207 PMCID: PMC8844509 DOI: 10.1093/molbev/msac026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
Collapse
Affiliation(s)
- Lin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xinxin Zhu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Weichen Huang
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
26
|
Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, Jia L, Lin HY, Xie L, Weng X, Dong C, Qian Q, Lin F, Xu H, Lu H, Cutti L, Chen H, Deng S, Guo L, Chuah TS, Song BK, Scarabel L, Qiu J, Zhu QH, Yu Q, Timko MP, Yamaguchi H, Merotto A, Qiu Y, Olsen KM, Fan L, Ye CY. Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nat Commun 2022; 13:689. [PMID: 35115514 PMCID: PMC8814039 DOI: 10.1038/s41467-022-28359-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
Collapse
Affiliation(s)
- Dongya Wu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Yu Feng
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Sangting Lao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Lei Jia
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Han-Yang Lin
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xifang Weng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Qinghong Qian
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Feng Lin
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Haiming Xu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Lu
- Institute of Maize and Upland Grain, Zhejiang Academy of Agricultural Sciences, Dongyang, 322105, China
| | - Luan Cutti
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Huajun Chen
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tse-Seng Chuah
- Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, 02600, Arau, Perlis, Malaysia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia
| | - Laura Scarabel
- Istituto per la Protezione Sostenibile delle Piante (IPSP), CNR, Viale dell'Università, 16, 35020, Legnaro (PD), Italy
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200235, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Yingxiong Qiu
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
27
|
Wu H, Yang JB, Liu JX, Li DZ, Ma PF. Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales. FRONTIERS IN PLANT SCIENCE 2022; 12:824672. [PMID: 35173754 PMCID: PMC8841755 DOI: 10.3389/fpls.2021.824672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
Collapse
Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
28
|
Casola C, Li J. Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C 4 plants. PeerJ 2022; 10:e12791. [PMID: 35127287 PMCID: PMC8801178 DOI: 10.7717/peerj.12791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. METHODS Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. RESULTS The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacements in C4 lineages, with both RbcL and RpoC1 (the RNA polymerase beta' subunit 1) showing a significantly higher convergent/non-convergent replacements ratio in C4 branches. Notably, more C4:C4 reference branches showed higher numbers of convergent vs. non-convergent replacements than C3:C3 and C3:C4 branches. Our results suggest that, in the PACMAD clade, C4 grasses experienced higher levels of molecular convergence than C3 species across multiple chloroplast genes. These findings have important implications for our understanding of the evolution of the C4 photosynthesis pathway.
Collapse
Affiliation(s)
- Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
- Interdisciplinary Graduate Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States of America
| | - Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
29
|
Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). BIOLOGY 2022; 11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.
Collapse
Affiliation(s)
| | | | - Xue-Jie Zhang
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| |
Collapse
|
30
|
Ren J, Tian J, Jiang H, Zhu XX, Mutie FM, Wanga VO, Ding SX, Yang JX, Dong X, Chen LL, Cai XZ, Hu GW. Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus. FRONTIERS IN PLANT SCIENCE 2022; 13:828467. [PMID: 35283921 PMCID: PMC8908325 DOI: 10.3389/fpls.2022.828467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/31/2022] [Indexed: 05/13/2023]
Abstract
Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Coleanthus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it is protected at international and national levels. In this study, we sequenced its whole chloroplast genome for the first time using the next-generation sequencing (NGS) technology on the Illumina platform, and performed a comparative and phylogenetic analysis with the related species in Poaceae. The complete chloroplast genome of C. subtilis is 135,915 bp in length, with a quadripartite structure having two 21,529 bp inverted repeat regions (IRs) dividing the entire circular genome into a large single copy region (LSC) of 80,100 bp and a small single copy region (SSC) of 12,757 bp. The overall GC content is 38.3%, while the GC contents in LSC, SSC, and IR regions are 36.3%, 32.4%, and 43.9%, respectively. A total of 129 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The accD gene and the introns of both clpP and rpoC1 genes were missing. In addition, the ycf1, ycf2, ycf15, and ycf68 were pseudogenes. Although the chloroplast genome structure of C. subtilis was found to be conserved and stable in general, 26 SSRs and 13 highly variable loci were detected, these regions have the potential to be developed as important molecular markers for the subfamily Pooideae. Phylogenetic analysis with species in Poaceae indicated that Coleanthus and Phippsia were sister groups, and provided new insights into the relationship between Coleanthus, Zingeria, and Colpodium. This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin.
Collapse
Affiliation(s)
- Jing Ren
- College of Life Sciences, Hunan Normal University, Changsha, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jing Tian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Zhu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Xiong Ding
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling-Ling Chen
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiu-Zhen Cai
- College of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Xiu-Zhen Cai,
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Guang-Wan Hu,
| |
Collapse
|
31
|
Ferreira RCU, da Costa Lima Moraes A, Chiari L, Simeão RM, Vigna BBZ, de Souza AP. An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures. FRONTIERS IN PLANT SCIENCE 2021; 12:770461. [PMID: 34966402 PMCID: PMC8710810 DOI: 10.3389/fpls.2021.770461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
Collapse
Affiliation(s)
| | - Aline da Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
32
|
Oliveira MAS, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques Da Silva SS, Oliveira RS, Simon MF, Lima GSA, Gissi DS, Almeida CCDS, Souza G, Marques A. High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae). Front Genet 2021; 12:727314. [PMID: 34630521 PMCID: PMC8495327 DOI: 10.3389/fgene.2021.727314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
Collapse
Affiliation(s)
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | | | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | | | - Ronaldo Simão Oliveira
- Campus Xique Xique, Federal Institute of Education, Science and Technology of Bahia, Xique-Xique, Brazil
| | | | - Gaus S A Lima
- Center of Agronomic Sciences, Federal University of Alagoas, Rio Largo, Brazil
| | - Danilo Soares Gissi
- Department of Biostatistics, Institute of Biosciences-IBB, Plant Biology, Parasitology and Zoology, São Paulo State University-UNESP, Botucatu, Brazil
| | | | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil.,Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| |
Collapse
|
33
|
Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Streptochaeta Genome and the Evolution of the Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:710383. [PMID: 34671369 PMCID: PMC8521107 DOI: 10.3389/fpls.2021.710383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/08/2021] [Indexed: 05/15/2023]
Abstract
In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
Collapse
Affiliation(s)
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | | | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| |
Collapse
|
34
|
Meena RK, Negi N, Uniyal N, Bhandari MS, Sharma R, Ginwal HS. Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum. J Genet 2021. [DOI: 10.1007/s12041-021-01273-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
35
|
Feng LY, Shi C, Gao LZ. The complete chloroplast genome sequence of Bromus catharticus Vahl. (Poaceae). Mitochondrial DNA B Resour 2021; 6:2825-2827. [PMID: 34514141 PMCID: PMC8425758 DOI: 10.1080/23802359.2021.1970646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Bromus catharticus Vahl. belongs to the Pooideae subfamily of Poaceae. In this study, we sequenced and assembled the complete chloroplast genome of B. catharticus. The complete chloroplast genome was 134,718 bp in size, including a large single-copy region of 80,540 bp, a small single-copy region of 11,806 bp and a pair of reverse repeats of 21,186 bp in size. The annotation of B. catharticus indicates that it contained 89 protein-coding genes, 47 tRNA genes and eight rRNA genes. Our phylogenetic analysis of all protein-coding genes of the 36 grass complete chroloplast genomes using Cyperus rotundus as outgroup showed that B. catharticus is closely related to the Koeleria and Avena species to form the Pooideae lineage of the grass family.
Collapse
Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Chao Shi
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China.,Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
36
|
Feng LY, Gao LZ. Characterization of the chloroplast genome sequence of Bonia amplexicaulis (L.C.Chia, H.L.Fung & Y.L.Yang) N.H.Xia (Poaceae). Mitochondrial DNA B Resour 2021; 6:2822-2824. [PMID: 34514140 PMCID: PMC8425685 DOI: 10.1080/23802359.2021.1972871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Bonia amplexicaulis (L.C.Chia, H.L.Fung & Y.L.Yang) N.H.Xia is a member of the Bambusoideae subfamily in Poaceae. In this study, we sequenced, assembled and characterized the complete chloroplast genome of B. amplexicaulis. The complete chloroplast genome was 139,935 bp in size, including a large single copy region of 83,453 bp, a small single-copy region of 12,860 bp and a pair of reverse repeats of 21,811 bp in size. The annotation of the B. amplexicaulis chloroplast genome indicates that it contained 83 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Our phylogenetic analysis of all protein-coding genes from the 36 complete chroloplast grass genomes using Cyperus rotundus as outgroup showed that B. amplexicaulis is closely related to Otatea glauca and Pariana campestris to form the Bambusoideae lineage of the grass family.
Collapse
Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| |
Collapse
|
37
|
Bhatt P, Thaker V. A comparative study on 193 plastomes of Poaceae for validity and implications of individual barcode genes and concatenated protein coding sequences with selected plastomes of grasses from the desert of India. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100921] [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] Open
|
38
|
Escobar-Correas S, Broadbent JA, Andraszek A, Stockwell S, Howitt CA, Juhász A, Colgrave ML. Perennial Ryegrass Contains Gluten-Like Proteins That Could Contaminate Cereal Crops. Front Nutr 2021; 8:708122. [PMID: 34395501 PMCID: PMC8355629 DOI: 10.3389/fnut.2021.708122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022] Open
Abstract
Background: To ensure safe consumption of gluten-free products, there is a need to understand all sources of unintentional contamination with gluten in the food chain. In this study, ryegrass (Lolium perenne), a common weed infesting cereal crop, is analysed as a potential source of gluten-like peptide contamination. Materials and Methods: Ten ryegrass cultivars were analysed using shotgun proteomics for the presence of proteins from the prolamin superfamily. A relative quantitative assay was developed to detect ryegrass gluten-like peptides in comparison with those found in 10 common wheat cultivars. Results: A total of 19 protein accessions were found across 10 cultivars of ryegrass for the protein families of PF00234-Tryp_alpha_amyl, PF13016-Gliadin, and PF03157-Glutenin_HMW. Protein and peptide homology searches revealed that gliadin-like peptides were similar to avenin and gamma-gliadin peptides. A total of 20 peptides, characteristic of prolamin superfamily proteins, were selected for liquid chromatography mass spectrometry (LC-MS) with multiple reaction monitoring (MRM). Only two of the monitored peptides were detected with high abundance in wheat, and all others were detected in ryegrass. Glutenin and alpha-amylase/trypsin inhibitor peptides were reported for the first time in ryegrass and were noted to be conserved across the Poaceae family. Conclusion: A suite of gluten-like peptides were identified using proteomics that showed consistent abundance across ryegrass cultivars but were not detected in wheat cultivars. These peptides will be useful for differentiating wheat gluten contamination from ryegrass gluten contamination.
Collapse
Affiliation(s)
- Sophia Escobar-Correas
- CSIRO Agriculture and Food, St. Lucia, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | | | | | | | | | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, St. Lucia, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| |
Collapse
|
39
|
Cheon SH, Woo MA, Jo S, Kim YK, Kim KJ. The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae). PLANTS 2021; 10:plants10081517. [PMID: 34451562 PMCID: PMC8400354 DOI: 10.3390/plants10081517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022]
Abstract
The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.
Collapse
|
40
|
Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
Collapse
Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
41
|
Ren Y, Xia H, Lu L, Zhao G. Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1852-1854. [PMID: 34124367 PMCID: PMC8183546 DOI: 10.1080/23802359.2021.1935343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/23/2021] [Indexed: 12/19/2022] Open
Abstract
In the present study, the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum was sequenced, assembled and compared with closely related species. The chloroplast genome of Hordeum vulgare L. var. trifurcatum was composed of 84 protein-coding genes (PCG), 8 ribosomal RNA (rRNA) genes, and 38 transfer RNA (tRNA) genes. The Hordeum vulgare L. var. trifurcatum chloroplast genome is 136,485 bp in size, with the GC content of 38.32%. Phylogenetic analysis based on the combined chloroplast gene dataset indicated that the Hordeum vulgare L. var. trifurcatum exhibited a close relationship with Hordeum vulgare subsp. spontaneum and Hordeum vulgare subsp. vulgare.
Collapse
Affiliation(s)
- Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
| | - Hu Xia
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
| | - Lidan Lu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
| |
Collapse
|
42
|
Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. Sci Rep 2021; 11:11731. [PMID: 34083611 PMCID: PMC8175739 DOI: 10.1038/s41598-021-91071-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.
Collapse
|
43
|
Delgado-González CR, Madariaga-Navarrete A, Fernández-Cortés JM, Islas-Pelcastre M, Oza G, Iqbal HMN, Sharma A. Advances and Applications of Water Phytoremediation: A Potential Biotechnological Approach for the Treatment of Heavy Metals from Contaminated Water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5215. [PMID: 34068925 PMCID: PMC8157233 DOI: 10.3390/ijerph18105215] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 02/05/2023]
Abstract
Potable and good-quality drinking water availability is a serious global concern, since several pollution sources significantly contribute to low water quality. Amongst these pollution sources, several are releasing an array of hazardous agents into various environmental and water matrices. Unfortunately, there are not very many ecologically friendly systems available to treat the contaminated environment exclusively. Consequently, heavy metal water contamination leads to many diseases in humans, such as cardiopulmonary diseases and cytotoxicity, among others. To solve this problem, there are a plethora of emerging technologies that play an important role in defining treatment strategies. Phytoremediation, the usage of plants to remove contaminants, is a technology that has been widely used to remediate pollution in soils, with particular reference to toxic elements. Thus, hydroponic systems coupled with bioremediation for the removal of water contaminants have shown great relevance. In this review, we addressed several studies that support the development of phytoremediation systems in water. We cover the importance of applied science and environmental engineering to generate sustainable strategies to improve water quality. In this context, the phytoremediation capabilities of different plant species and possible obstacles that phytoremediation systems may encounter are discussed with suitable examples by comparing different mechanistic processes. According to the presented data, there are a wide range of plant species with water phytoremediation potential that need to be studied from a multidisciplinary perspective to make water phytoremediation a viable method.
Collapse
Affiliation(s)
- Cristián Raziel Delgado-González
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo 43600, Mexico; (C.R.D.-G.); (A.M.-N.); (M.I.-P.)
| | - Alfredo Madariaga-Navarrete
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo 43600, Mexico; (C.R.D.-G.); (A.M.-N.); (M.I.-P.)
| | - José Miguel Fernández-Cortés
- Centre of Bioengineering, School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo 76130, Mexico;
| | - Margarita Islas-Pelcastre
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo 43600, Mexico; (C.R.D.-G.); (A.M.-N.); (M.I.-P.)
| | - Goldie Oza
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Parque Tecnológico, Pedro Escobedo 76703, Mexico;
| | - Hafiz M. N. Iqbal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Ashutosh Sharma
- Centre of Bioengineering, School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo 76130, Mexico;
| |
Collapse
|
44
|
Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA. PLoS One 2021; 16:e0249735. [PMID: 33857196 PMCID: PMC8049495 DOI: 10.1371/journal.pone.0249735] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/23/2021] [Indexed: 11/19/2022] Open
Abstract
Multidomain proteins can have a complex evolutionary history that may involve de novo domain evolution, recruitment and / or recombination of existing domains and domain losses. Here, the domain evolution of the plant-specific Ca2+-permeable mechanosensitive channel protein, MID1-COMPLEMENTING ACTIVITY (MCA), was investigated. MCA, a multidomain protein, possesses a Ca2+-influx-MCAfunc domain and a PLAC8 domain. Profile Hidden Markov Models (HMMs) of domains were assessed in 25 viridiplantae proteomes. While PLAC8 was detected in plants, animals, and fungi, MCAfunc was found in streptophytes but not in chlorophytes. Full MCA proteins were only found in embryophytes. We identified the MCAfunc domain in all streptophytes including charophytes where it appeared in E3 ubiquitin ligase-like proteins. Our Maximum Likelihood (ML) analyses suggested that the MCAfunc domain evolved early in the history of streptophytes. The PLAC8 domain showed similarity to Plant Cadmium Resistance (PCR) genes, and the coupling of MCAfunc and PLAC8 seemed to represent a single evolutionary event. This combination is unique in MCA, and does not exist in other plant mechanosensitive channels. Within angiosperms, gene duplications increased the number of MCAs. Considering their role in mechanosensing in roots, MCA might be instrumental for the rise of land plants. This study provides a textbook example of de novo domain emergence, recombination, duplication, and losses, leading to the convergence of function of proteins in plants.
Collapse
|
45
|
Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| |
Collapse
|
46
|
Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 2021; 9:e10886. [PMID: 33665028 PMCID: PMC7912680 DOI: 10.7717/peerj.10886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.
Collapse
Affiliation(s)
- Benoit Loeuille
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Verônica Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America
| | - Sonia Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - José Rubens Pirani
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| |
Collapse
|
47
|
Orton LM, Barberá P, Nissenbaum MP, Peterson PM, Quintanar A, Soreng RJ, Duvall MR. A 313 plastome phylogenomic analysis of Pooideae: Exploring relationships among the largest subfamily of grasses. Mol Phylogenet Evol 2021; 159:107110. [PMID: 33609709 DOI: 10.1016/j.ympev.2021.107110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae). We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the "mask alignment" tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.
Collapse
Affiliation(s)
- Lauren M Orton
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA.
| | - Patricia Barberá
- Department of Africa and Madagascar, Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Matthew P Nissenbaum
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Paul M Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Alejandro Quintanar
- Herbario MA, Unidad de Herbarios, Real Jardín Botánico de Madrid CSIC, 28014 Madrid, Spain
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Melvin R Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA; Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| |
Collapse
|
48
|
Li W, Shi C, Li K, Zhang QJ, Tong Y, Zhang Y, Wang J, Clark L, Gao LZ. Draft genome of the herbaceous bamboo Raddia distichophylla. G3-GENES GENOMES GENETICS 2021; 11:6066164. [PMID: 33585868 PMCID: PMC8022951 DOI: 10.1093/g3journal/jkaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022]
Abstract
Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide.
Collapse
Affiliation(s)
- Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Kui Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Jun Wang
- Institution of Sustainable Development, Southwest China Forestry University, Kunming 650224, China
| | - Lynn Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011-1020, USA
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| |
Collapse
|
49
|
Tkach N, Nobis M, Schneider J, Becher H, Winterfeld G, Jacobs SWL, Röser M. Molecular Phylogenetics and Micromorphology of Australasian Stipeae (Poaceae, Subfamily Pooideae), and the Interrelation of Whole-Genome Duplication and Evolutionary Radiations in This Grass Tribe. FRONTIERS IN PLANT SCIENCE 2021; 11:630788. [PMID: 33552114 PMCID: PMC7862344 DOI: 10.3389/fpls.2020.630788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
The mainly Australian grass genus Austrostipa (tribe Stipeae) comprising approximately 64 species represents a remarkable example of an evolutionary radiation. To investigate aspects of diversification, macro- and micromorphological variation in this genus, we conducted molecular phylogenetic and scanning electron microscopy (SEM) analyses including representatives from most of Austrostipa's currently accepted subgenera. Because of its taxonomic significance in Stipeae, we studied the lemma epidermal pattern (LEP) in 34 representatives of Austrostipa. Plastid DNA variation within Austrostipa was low and only few lineages were resolved. Nuclear ITS and Acc1 yielded comparable groupings of taxa and resolved subgenera Arbuscula, Petaurista, and Bambusina in a common clade and as monophyletic. In most of the Austrostipa species studied, the LEP was relatively uniform (typical maize-like), but six species had a modified cellular structure. The species representing subgenera Lobatae, Petaurista, Bambusina as well as A. muelleri from subg. Tuberculatae were well-separated from all the other species included in the analysis. We suggest recognizing nine subgenera in Austrostipa (with number of species): Arbuscula (4), Aulax (2), Austrostipa (36), Bambusina (2), Falcatae (10), Lobatae (5), Longiaristatae (2), Petaurista (2) and the new subgenus Paucispiculatae (1) encompassing A. muelleri. Two paralogous sequence copies of Acc1, forming two distinct clades, were found in polyploid Austrostipa and Anemanthele. We found analogous patterns for our samples of Stipa s.str. with their Acc1 clades strongly separated from those of Austrostipa and Anemanthele. This underlines a previous hypothesis of Tzvelev (1977) that most extant Stipeae are of hybrid origin. We also prepared an up-to-date survey and reviewed the chromosome number variation for our molecularly studied taxa and the whole tribe Stipeae. The chromosome base number patterns as well as dysploidy and whole-genome duplication events were interpreted in a phylogenetic framework. The rather coherent picture of chromosome number variation underlines the enormous phylogenetic and evolutionary significance of this frequently ignored character.
Collapse
Affiliation(s)
- Natalia Tkach
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Julia Schneider
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | - Hannes Becher
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Grit Winterfeld
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | | | - Martin Röser
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| |
Collapse
|
50
|
Botnen SS, Thoen E, Eidesen PB, Krabberød AK, Kauserud H. Community composition of arctic root-associated fungi mirrors host plant phylogeny. FEMS Microbiol Ecol 2020; 96:fiaa185. [PMID: 32918451 PMCID: PMC7840110 DOI: 10.1093/femsec/fiaa185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.
Collapse
Affiliation(s)
- S S Botnen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
- The University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway
- Oslo Metropolitan University, PO Box 4 St. Olavs plass, NO-0130 Oslo, Norway
| | - E Thoen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - P B Eidesen
- The University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway
| | - A K Krabberød
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - H Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| |
Collapse
|