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Liu JX, Guo C, Ma PF, Zhou MY, Luo YH, Zhu GF, Xu ZC, Milne RI, Vorontsova MS, Li DZ. The origin and morphological character evolution of the paleotropical woody bamboos. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39166548 DOI: 10.1111/jipb.13751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 08/23/2024]
Abstract
The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time-calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene-Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.
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Affiliation(s)
- Jing-Xia Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Cen Guo
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya-Huang Luo
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guang-Fu Zhu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | | | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Zhao R, Huang N, Zhang Z, Luo W, Xiang J, Xu Y, Wang Y. Genetic Diversity Analysis and Prediction of Potential Suitable Areas for the Rare and Endangered Wild Plant Henckelia longisepala. PLANTS (BASEL, SWITZERLAND) 2024; 13:2093. [PMID: 39124211 PMCID: PMC11314309 DOI: 10.3390/plants13152093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024]
Abstract
Henckelia longisepala (H. W. Li) D. J. Middleton & Mich. Möller is a rare and endangered plant species found only in Southeastern Yunnan, China, and Northern Vietnam. It is listed as a threatened species in China and recognized as a plant species with extremely small populations (PSESP), while also having high ornamental value and utilization potential. This study used ddRAD-seq technology to quantify genetic diversity and structure for 32 samples from three extant populations of H. longisepala. The H. longisepala populations were found to have low levels of genetic diversity (Ho = 0.1216, He = 0.1302, Pi = 0.1731, FIS = 0.1456), with greater genetic differentiation observed among populations (FST = 0.3225). As indicated by genetic structure and phylogenetic analyses, samples clustered into three distinct genetic groups that corresponded to geographically separate populations. MaxEnt modeling was used to identify suitable areas for H. longisepala across three time periods and two climate scenarios (SSP1-2.6, SSP5-8.5). High-suitability areas were identified in Southeastern Yunnan Province, Northern Vietnam, and Eastern Laos. Future H. longisepala distribution was predicted to remain centered in these areas, but with a decrease in the total amount of suitable habitat. The present study provides key data on H. longisepala genetic diversity, as well as a theoretical basis for the conservation, development, and utilization of its germplasm resources.
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Affiliation(s)
- Renfen Zhao
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
| | - Nian Huang
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
| | - Zhiyan Zhang
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
| | - Wei Luo
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
| | - Jianying Xiang
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming 650224, China
| | - Yuanjie Xu
- College of Soil and Water Conservation, Southwest Forestry University, Kunming 650224, China
| | - Yizhi Wang
- College of Forestry, Southwest Forestry University, Kunming 650224, China; (R.Z.); (N.H.); (Z.Z.); (W.L.); (J.X.)
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming 650224, China
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Hu XZ, Guo C, Qin SY, Li DZ, Guo ZH. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae). PLANT DIVERSITY 2024; 46:344-352. [PMID: 38798728 PMCID: PMC11119509 DOI: 10.1016/j.pld.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 05/29/2024]
Abstract
Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
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Affiliation(s)
- Xiang-Zhou Hu
- 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
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Sheng-Yuan Qin
- 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
| | - 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
| | - Zhen-Hua Guo
- 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
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Xu X, Wu M, Gou G, Wei T, Yang D, Dai Z. The complete chloroplast genome of Dendrocalamus liboensis Hsueh & D. Z. Li 1985 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:158-162. [PMID: 38274849 PMCID: PMC10810639 DOI: 10.1080/23802359.2024.2306204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Dendrocalamus liboensis Hsueh & D. Z. Li 1985 is a unique member of the Bambusoideae subfamily found in Guizhou, China. The species has both economic importance and ornamental value. This study represents the first report of the sequencing and assembly of the complete chloroplast genome of D. liboensis. The total length of the genome was 139,483 bp, with a conventional quadripartite framework consisting of a large single-copy (LSC) region (83,001 bp in length), a small single-copy (SSC) region (12,896 bp in length), and two inverted repeats (IR) regions (both 21,793 bp in length). Overall, the D. liboensis chloroplast genome contained 128 functional genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis showed that D. liboensis closely resembled D. sapidus, with both found on a strongly supported branch of the phylogenetic tree.
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Affiliation(s)
- Xue Xu
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | - Mingli Wu
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | - Guangqian Gou
- College of Life Sciences/Institute of Agro-bioengineering, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education), Guizhou University, Guiyang, China
| | | | | | - Zhaoxia Dai
- College of Forestry, Guizhou University, Guiyang, China
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Cai ZY, Niu ZY, Zhang YY, Tong YH, Vu TC, Goh WL, Sungkaew S, Teerawatananon A, Xia NH. Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae). FRONTIERS IN PLANT SCIENCE 2023; 14:1274337. [PMID: 38111884 PMCID: PMC10726129 DOI: 10.3389/fpls.2023.1274337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023]
Abstract
Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.
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Affiliation(s)
- Zhuo-Yu Cai
- Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- South China National Botanical Garden, Guangzhou, China
| | - Zheng-Yang Niu
- Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- South China National Botanical Garden, Guangzhou, China
| | - You-Yuan Zhang
- Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Quality Management Office, Guiyang Vocational and Technical College, Guiyang, China
| | - Yi-Hua Tong
- Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tien Chinh Vu
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Wei Lim Goh
- Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, Malaysia
| | - Sarawood Sungkaew
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | - Nian-He Xia
- Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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Liu JX, Xu ZC, Zhang YX, Zhou MY, Li DZ. The identity of Dinochloa species and enumeration of Melocalamus (Poaceae: Bambusoideae) in China. PLANT DIVERSITY 2023; 45:133-146. [PMID: 37069933 PMCID: PMC10105079 DOI: 10.1016/j.pld.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 06/19/2023]
Abstract
Three woody bamboo species collected in Hainan, China in 1940 have been described as Dinochloa based on vegetative specimens. However, the identity of these species has long been in doubt, largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus, a climbing or scrambling bamboo genus of the paleotropical woody bamboos (Poaceae: Bambusoideae) that consists of about 15 species and one variety. To determine the phylogenetic affinity of the three Dinochloa species from Hainan, we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera, performed molecular phylogenetic analysis, and compared their morphology based on herbarium and fieldwork investigation. Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus, not Dinochloa. Morphological analysis showed that these three species have a climbing habit but do not grow spirally, their culm leaves have smooth bases, and there is a ring of powder and/or tomenta above and below the nodes. Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus, i.e., Melocalamus orenudus (McClure) D.Z. Li & J.X. Liu, Melocalamus puberulus (McClure) D.Z. Li & J.X. Liu, and Melocalamus utilis (McClure) D.Z. Li & J.X. Liu, respectively. This study concludes with an enumeration of Chinese species of Melocalamus, with a key to nine recognized species and one variety, and a lectotypification for M. compatiflorus.
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Affiliation(s)
- Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - 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
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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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.
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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
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Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species. Genes (Basel) 2022; 13:genes13091519. [PMID: 36140690 PMCID: PMC9498922 DOI: 10.3390/genes13091519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.
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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.
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Chalopin D, Clark LG, Wysocki WP, Park M, Duvall MR, Bennetzen JL. Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae). FRONTIERS IN PLANT SCIENCE 2021; 12:725728. [PMID: 34567039 PMCID: PMC8456298 DOI: 10.3389/fpls.2021.725728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.
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Affiliation(s)
- Domitille Chalopin
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - William P. Wysocki
- Center for Translational Data Science, University of Chicago, Chicago, IL, United States
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Melvin R. Duvall
- Department of Biology and Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, IL, United States
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Tang SL, Xie JH, Cai JZ. The complete plastid genome of Thyrsostachys siamensis (Poaceae, Bambusoideae). Mitochondrial DNA B Resour 2021; 6:1781-1783. [PMID: 34104773 PMCID: PMC8168764 DOI: 10.1080/23802359.2021.1934138] [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: 11/01/2022] Open
Abstract
Thyrsostachys is oligotypic genus of Bambusinae, while its phylogenetic position had been unclear. Here, the complete plastid genome of the type species, T. siamensis, was sequenced and analyzed in this work. The complete genome is a typical quadripartite structure with 139,522 bp in length, comprising of a large single-copy region (LSC, 83,032 bp), a small single-copy region (SSC, 12,892 bp), and a pair of invert repeats regions (IR, 21,799 bp). The genome contains 138 genes, 89 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. The GC content of genome was 38.9%. Phylogenetic analysis indicated T. siamensis was sister to Dendrocalamus birmanicus within Bambusinae.
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Affiliation(s)
- Shu-Ling Tang
- College of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou, China
| | - Jian-Hua Xie
- College of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou, China
| | - Jia-Zhen Cai
- College of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou, China
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Zhang Y, De Meyer M, Virgilio M, Feng S, Badji K, Li Z. Phylogenomic resolution of the Ceratitis FARQ complex (Diptera: Tephritidae). Mol Phylogenet Evol 2021; 161:107160. [PMID: 33794396 DOI: 10.1016/j.ympev.2021.107160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
The Ceratitis FARQ complex (formerly FAR complex) includes four frugivorous tephritids, Ceratitis fasciventris, C. anonae, C. rosa and C. quilicii, the latter two causing important agricultural losses in Africa. Although FARQ species can be identified on the basis of subtle morphological differences, they cannot be resolved as monophyletic when trying phylogenetic tree reconstructions based on mitochondrial or nuclear gene fragments except for microsatellites. In this study, we used mitogenome and genome-wide SNPs to investigate the phylogenetic relationship within the complex as well as between all four Ceratitis subgenera. The analysis of 13 species supported the monophyly of the Ceratitis subgenera Ceratitis, Ceratalaspis, Pardalaspis, and recovered Pterandrus as paraphyletic but could not properly resolve species within the FARQ complex. Conversely, gene and species tree reconstructions based on 785,484 genome-wide SNPs could consistently resolve the FARQ taxa and provide insights into their phylogenetic relationships. Gene flow was detected by TreeMix analysis from C. quilicii to C. fasciventris, suggesting the existence of introgression events in the FARQ complex. Our results suggest that genome-wide SNPs represent a suitable tool for the molecular diagnosis of FARQ species and could possibly be used to develop rapid diagnostic methods or to trace the origins of intercepted samples.
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Affiliation(s)
- Yue Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Marc De Meyer
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Shiqian Feng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Kemo Badji
- Crop Protection Directorate, Dakar, Senegal.
| | - Zhihong Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Wang R, Liu K, Zhang XJ, Chen WL, Qu XJ, Fan SJ. Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:638597. [PMID: 33841465 PMCID: PMC8030268 DOI: 10.3389/fpls.2021.638597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.
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Affiliation(s)
- Rong Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Kuan Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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Xu ZC, Liu JX, Li DZ. Gigantochloa glabrata (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China. PHYTOKEYS 2021; 171:37-45. [PMID: 33510574 PMCID: PMC7809009 DOI: 10.3897/phytokeys.171.59562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Gigantochloa glabrata N. H. Xia & Y. Zeng ex D. Z. Li & Z. C. Xu, sp. nov., a new species of paleotropical woody bamboo has been described and illustrated from Yunnan, China. The new species is morphologically similar to G. albociliata and G. levis, but differs from them by having erect culm sheath blades; culm sheath ligules 4-6 mm high, truncate, denticulate; and with a ring of white tomentum on the intranode and below the node. The new species was mistakenly identified as Gigantochloa albociliata in the Flora of China and was recognised with description of the vegetative characters in 2014, but it was not effectively published. Here, we designate a complete specimen with inflorescence as the type and describe it in accordance with the Code.
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Affiliation(s)
- Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaKunming Institute of BotanyKunmingChina
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaUniversity of the Chinese Academy of SciencesKunmingChina
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaKunming Institute of BotanyKunmingChina
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaUniversity of the Chinese Academy of SciencesKunmingChina
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaKunming Institute of BotanyKunmingChina
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaUniversity of the Chinese Academy of SciencesKunmingChina
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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