Analysis of an improved Cyanophora paradoxa genome assembly
Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model g...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2020
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/142287 |
| _version_ | 1811687706453868544 |
|---|---|
| author | Price, Dana C. Goodenough, Ursula W. Roth, Robyn Lee, Jae-Hyeok Kariyawasam, Thamali Mutwil, Marek Ferrari, Camilla Facchinelli, Fabio Ball, Steven G. Cenci, Ugo Chan, Cheong Xin Wagner, Nicole E. Yoon, Hwan Su Weber, Andreas P. M. Bhattacharya, Debashish |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Price, Dana C. Goodenough, Ursula W. Roth, Robyn Lee, Jae-Hyeok Kariyawasam, Thamali Mutwil, Marek Ferrari, Camilla Facchinelli, Fabio Ball, Steven G. Cenci, Ugo Chan, Cheong Xin Wagner, Nicole E. Yoon, Hwan Su Weber, Andreas P. M. Bhattacharya, Debashish |
| author_sort | Price, Dana C. |
| collection | NTU |
| description | Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage. |
| first_indexed | 2024-10-01T05:20:34Z |
| format | Journal Article |
| id | ntu-10356/142287 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:20:34Z |
| publishDate | 2020 |
| record_format | dspace |
| spelling | ntu-10356/1422872023-02-28T17:02:30Z Analysis of an improved Cyanophora paradoxa genome assembly Price, Dana C. Goodenough, Ursula W. Roth, Robyn Lee, Jae-Hyeok Kariyawasam, Thamali Mutwil, Marek Ferrari, Camilla Facchinelli, Fabio Ball, Steven G. Cenci, Ugo Chan, Cheong Xin Wagner, Nicole E. Yoon, Hwan Su Weber, Andreas P. M. Bhattacharya, Debashish School of Biological Sciences Science::Biological sciences Cyanophora Paradoxa Archaeplastida Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage. Published version 2020-06-18T06:31:36Z 2020-06-18T06:31:36Z 2019 Journal Article Price, D. C., Goodenough, U. W., Roth, R., Lee, J.-H., Kariyawasam, T., Mutwil, M., . . . Bhattacharya, D. (2019). Analysis of an improved Cyanophora paradoxa genome assembly. DNA Research, 26(4), 287-299. doi:10.1093/dnares/dsz009 1340-2838 https://hdl.handle.net/10356/142287 10.1093/dnares/dsz009 31098614 2-s2.0-85071701620 4 26 287 299 en DNA Research © 2019 The Author(s). Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. application/pdf |
| spellingShingle | Science::Biological sciences Cyanophora Paradoxa Archaeplastida Price, Dana C. Goodenough, Ursula W. Roth, Robyn Lee, Jae-Hyeok Kariyawasam, Thamali Mutwil, Marek Ferrari, Camilla Facchinelli, Fabio Ball, Steven G. Cenci, Ugo Chan, Cheong Xin Wagner, Nicole E. Yoon, Hwan Su Weber, Andreas P. M. Bhattacharya, Debashish Analysis of an improved Cyanophora paradoxa genome assembly |
| title | Analysis of an improved Cyanophora paradoxa genome assembly |
| title_full | Analysis of an improved Cyanophora paradoxa genome assembly |
| title_fullStr | Analysis of an improved Cyanophora paradoxa genome assembly |
| title_full_unstemmed | Analysis of an improved Cyanophora paradoxa genome assembly |
| title_short | Analysis of an improved Cyanophora paradoxa genome assembly |
| title_sort | analysis of an improved cyanophora paradoxa genome assembly |
| topic | Science::Biological sciences Cyanophora Paradoxa Archaeplastida |
| url | https://hdl.handle.net/10356/142287 |
| work_keys_str_mv | AT pricedanac analysisofanimprovedcyanophoraparadoxagenomeassembly AT goodenoughursulaw analysisofanimprovedcyanophoraparadoxagenomeassembly AT rothrobyn analysisofanimprovedcyanophoraparadoxagenomeassembly AT leejaehyeok analysisofanimprovedcyanophoraparadoxagenomeassembly AT kariyawasamthamali analysisofanimprovedcyanophoraparadoxagenomeassembly AT mutwilmarek analysisofanimprovedcyanophoraparadoxagenomeassembly AT ferraricamilla analysisofanimprovedcyanophoraparadoxagenomeassembly AT facchinellifabio analysisofanimprovedcyanophoraparadoxagenomeassembly AT ballsteveng analysisofanimprovedcyanophoraparadoxagenomeassembly AT cenciugo analysisofanimprovedcyanophoraparadoxagenomeassembly AT chancheongxin analysisofanimprovedcyanophoraparadoxagenomeassembly AT wagnernicolee analysisofanimprovedcyanophoraparadoxagenomeassembly AT yoonhwansu analysisofanimprovedcyanophoraparadoxagenomeassembly AT weberandreaspm analysisofanimprovedcyanophoraparadoxagenomeassembly AT bhattacharyadebashish analysisofanimprovedcyanophoraparadoxagenomeassembly |