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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). Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Htet AH, Makabe S, Takahashi H, Samuel PA, Sato YI, Nakamura I. A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species. Breed Sci 2022; 72:267-273. [PMID: 36408325 PMCID: PMC9653197 DOI: 10.1270/jsbbs.21075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/04/2022] [Indexed: 06/16/2023]
Abstract
Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.
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Affiliation(s)
- Aung Htut Htet
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - So Makabe
- BEX Co. Ltd., Itabashi-ku, Tokyo 173-0004, Japan
| | | | - Poku Aduse Samuel
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Yo-ichiro Sato
- Kyoto Washoku Institute, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
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Wang Y, Jiang W, Ye W, Fu C, Gitzendanner MA, Soltis PS, Soltis DE, Qiu Y. Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum. BMC Plant Biol 2018; 18:208. [PMID: 30249188 PMCID: PMC6154912 DOI: 10.1186/s12870-018-1429-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 09/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Tetrastigma hemsleyanum is of great medicinal importance and used as a model system to address the evolutionary history of warm-temperate evergreen (WTE) forest biomes in East Asia over Neogene time scales. However, further studies on the neutral and adaptive divergence processes of T. hemsleyanum are currently impeded by a lack of genomic resources. In this study, we de novo assembled and annotated a reference transcriptome for two cpDNA lineages (Central-South-East vs. Southwest) of T. hemsleyanum. We further used comparative genomic and multilocus coalescent approaches to investigate the tempo and mode of lineage diversification in T. hemsleyanum. RESULTS A total of 52,838 and 65,197 unigenes with an N50 of 1,667 and 1,841 bp for Central-South-East (CSE) and Southwest (SW) lineages, respectively, were recovered, and 6,692 putative orthologs were identified between the two lineages. Estimation of Ka/Ks ratios for these orthologs revealed that ten genes had Ka/Ks values significantly greater than 0.5 (P < 0.05), whereas 2,099 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. Based on three bioinformatic strategies, we identified a total of 1,018 single-copy nuclear genes (SCNGs) from the orthologs. We successfully designed eight nuclear gene primer pairs with high intraspecific variation (e.g. hT = 0.923, πT = 1.68×10-3), when surveyed across a subset of T. hemsleyanum individuals. Concordant with the previous cpDNA data, the haplotype networks constructed for most nuclear gene loci clearly identified the two lineages. A multilocus coalescence analysis suggested that the separation between the two lineages appears to have occurred during the mid-Pliocene. Despite their ancient divergence, both lineages experienced expansion at rather localized scales and have continued to exchange genes at a low rate. CONCLUSIONS This study demonstrated the utility of transcriptome sequencing as a basis for SCNG development in non-model species and the advantages of integrating multiple nuclear loci for phylogeographic and phylogenetic studies.
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Affiliation(s)
- Yihan Wang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 China
| | - Weimei Jiang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Wenqing Ye
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
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Cacho NI, Strauss SY. Single-copy nuclear gene primers for Streptanthus and other Brassicaceae from genomic scans, published data, and ESTs. Appl Plant Sci 2013; 1:apps.1200002. [PMID: 25202560 PMCID: PMC4103123 DOI: 10.3732/apps.1200002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/05/2013] [Indexed: 06/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY We report 11 primer sets for nine single-copy nuclear genes in Streptanthus and other Thelypodieae (Brassicaceae) and their utility at tribal-level and species-level phylogenetics in this poorly resolved group. • METHODS AND RESULTS We selected regions based on a cross-referenced matrix of previous studies and public Brassica expressed sequence tags. To design primers, we used alignments of low-depth-coverage Illumina sequencing of genomic DNA for two species of Brassica mapped onto Arabidopsis thaliana. We report several primer combinations for five regions that consistently amplified a single band and yielded high-quality sequences for at least 70% of the species assayed, and for four additional regions whose utility might be clade specific. • CONCLUSIONS Our primers will be useful in improving resolution at shallow depths across the Thelypodieae, and likely in other Brassicaceae.
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Affiliation(s)
- N. Ivalú Cacho
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California 95616-5294 USA
| | - Sharon Y. Strauss
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California 95616-5294 USA
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