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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Wu M, Zhang K, Yang X, Qian X, Li R, Wei J. Paracladopuschiangmaiensis (Podostemaceae), a new generic record for China and its complete plastid genome. PHYTOKEYS 2022; 195:1-13. [PMID: 35800211 PMCID: PMC9046368 DOI: 10.3897/phytokeys.195.82789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
The genus Paracladopus was established based on the type species P.chiangmaiensis in 2006. The two Paracladopus species are distributed in Thailand and Laos; however, neither of them has been documented in China to date. During our field work in 2020, we collected a river-weed in Wuzhi Mountain, Hainan Province of China. After checking the morphological characters, it was identified as P.chiangmaiensis. Then, we assembled and annotated its chloroplast genome based on the genome skimming data. The results showed that the complete chloroplast genome was 133,748 bp with 35% GC content, consisting of 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood tree constructed based on the matk genes showed that WuMS109 was clustered with P.chiangmaiensis (AB537420, AB698348) without base difference and together with the remains of Paracladopus formed a sister clade to Cladopus. This is the first report of P.chiangmaiensis that represents a new generic record for China. The discovery of this river-weed could lay the foundation for investigating their biogeographical patterns and species evolution in further studies.
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Affiliation(s)
- Mingsong Wu
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haikou 570311, Hainan, ChinaChinese Academy of Medical Sciences & Peking Union Medical CollegeHaikouChina
| | - Kai Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, ChinaHainan Normal UniversityHaikouChina
| | - Xinquan Yang
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haikou 570311, Hainan, ChinaChinese Academy of Medical Sciences & Peking Union Medical CollegeHaikouChina
| | - Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, ChinaFujian Agriculture and Forestry UniversityFuzhouChina
| | - Rongtao Li
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haikou 570311, Hainan, ChinaChinese Academy of Medical Sciences & Peking Union Medical CollegeHaikouChina
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haikou 570311, Hainan, ChinaChinese Academy of Medical Sciences & Peking Union Medical CollegeHaikouChina
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
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