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Maravilla AJ, Rosato M, Rosselló JA. Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:2541. [PMID: 34834904 PMCID: PMC8621592 DOI: 10.3390/plants10112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.
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Affiliation(s)
| | | | - Josep A. Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/Quart 80, E-46008 València, Spain; (A.J.M.); (M.R.)
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Chen JH, Huang Y, Brachi B, Yun QZ, Zhang W, Lu W, Li HN, Li WQ, Sun XD, Wang GY, He J, Zhou Z, Chen KY, Ji YH, Shi MM, Sun WG, Yang YP, Zhang RG, Abbott RJ, Sun H. Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot. Nat Commun 2019; 10:5230. [PMID: 31745089 PMCID: PMC6864086 DOI: 10.1038/s41467-019-13128-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/22/2019] [Indexed: 01/25/2023] Open
Abstract
The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.
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Affiliation(s)
- Jia-Hui Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China.
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, 650092, Kunming, Yunnan, P. R. China
| | | | - Quan-Zheng Yun
- Beijing Ori-Gene Science and Technology Co., Ltd, 102206, Beijing, P.R. China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Life Sciences, Peking University, 100871, Beijing, P.R. China
- School of Life Sciences, Peking University, 100871, Beijing, P.R. China
| | - Wei Lu
- School of Life Sciences, Peking University, 100871, Beijing, P.R. China
| | - Hong-Na Li
- Beijing Ori-Gene Science and Technology Co., Ltd, 102206, Beijing, P.R. China
| | - Wen-Qing Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Xu-Dong Sun
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Guang-Yan Wang
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Jun He
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Kai-Yun Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Yun-Heng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Ming-Ming Shi
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Wen-Guang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China
| | - Yong-Ping Yang
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China.
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China.
| | - Ren-Gang Zhang
- Beijing Ori-Gene Science and Technology Co., Ltd, 102206, Beijing, P.R. China
| | - Richard J Abbott
- School of Biology, University of St. Andrews, St. Andrews, Fife, KY16 9TH, UK.
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, P. R. China.
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Zhou HC, Pellerin RJ, Waminal NE, Yang TJ, Kim HH. Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat. Genes Genomics 2019; 41:839-847. [PMID: 30903554 DOI: 10.1007/s13258-019-00786-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/08/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days. OBJECTIVE To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem., Dendropanax morbiferus H. Lév., Eleutherococcus sessiliflorus (Rupr. Et Maxim.) Seem., Kalopanax septemlobus (Thunb. ex A.Murr.) Koidz. METHOD Pre-labelled oligoprobe (PLOP)-fluorescence in situ hybridization (FISH) was carried out. RESULTS The chromosome number of A. elata was 2n = 24, whereas that of the other three species of D. morbiferus, E. sessiliflorus, and K. septemlobus was 2n = 48, corresponding to diploid and tetraploid, respectively, based on the basic chromosome number x = 12 in Araliaceae. In all four species, one pair of 5S signals were detected in the proximal regions of the short arms of chromosome 3, whereas in K. septemlobus, the 5S rDNA signals localized in the subtelomeric region of short arm of chromosome 3, while all the 45S rDNA signals localized at the paracentromeric region of the short arm of chromosome 1. And the telomeric repeat signals were detected at the telomeric region of both short and long arms of most chromosomes. CONCLUSION The PLOP-FISH was very effective compared with conventional FISH method. These results provide useful comparative cytogenetic information to better understand the genome structure of each species and will be useful to trace the history of ginseng genomic constitution.
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Affiliation(s)
- Hui Chao Zhou
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea.
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Biotechnology for bioenergy dedicated trees: meeting future energy demands. ACTA ACUST UNITED AC 2017; 73:15-32. [DOI: 10.1515/znc-2016-0185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/26/2017] [Indexed: 11/15/2022]
Abstract
Abstract
With the increase in human demands for energy, purpose-grown woody crops could be part of the global renewable energy solution, especially in geographical regions where plantation forestry is feasible and economically important. In addition, efficient utilization of woody feedstocks would engage in mitigating greenhouse gas emissions, decreasing the challenge of food and energy security, and resolving the conflict between land use for food or biofuel production. This review compiles existing knowledge on biotechnological and genomics-aided improvements of biomass performance of purpose-grown poplar, willow, eucalyptus and pine species, and their relative hybrids, for efficient and sustainable bioenergy applications. This includes advancements in tree in vitro regeneration, and stable expression or modification of selected genes encoding desirable traits, which enhanced growth and yield, wood properties, site adaptability, and biotic and abiotic stress tolerance. Genetic modifications used to alter lignin/cellulose/hemicelluloses ratio and lignin composition, towards effective lignocellulosic feedstock conversion into cellulosic ethanol, are also examined. Biotech-trees still need to pass challengeable regulatory authorities’ processes, including biosafety and risk assessment analyses prior to their commercialization release. Hence, strategies developed to contain transgenes, or to mitigate potential transgene flow risks, are discussed.
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