干旱区生态环境知识资源中心(Arid): Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions

Arid

DOI	10.3389/fgene.2021.674783
	Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
	Scobeyeva, Victoria A.; Artyushin, Ilya V.; Krinitsina, Anastasiya A.; Nikitin, Pavel A.; Antipin, Maxim I.; Kuptsov, Sergei V.; Belenikin, Maxim S.; Omelchenko, Denis O.; Logacheva, Maria D.; Konorov, Evgenii A.; Samoilov, Andrey E.; Speranskaya, Anna S.
通讯作者	Scobeyeva, VA (corresponding author), Lomonosov Moscow State Univ, Dept Evolut, Fac Biol, Moscow, Russia. ; Scobeyeva, VA (corresponding author), Moscow Inst Phys & Technol, Dept Mol & Biol Phys, Dolgoprudnyi, Russia.
来源期刊	FRONTIERS IN GENETICS
EISSN	1664-8021
出版年	2021
卷号	12
英文摘要	Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus-Allium-is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes' annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the normal or pseudo state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
英文关键词	Allium plastome sequence evolution pseudogenization
类型	Article
语种	英语
开放获取类型	gold, Green Published
收录类别	SCI-E
WOS记录号	WOS:000675511200001
WOS关键词	COMPLETE PLASTID GENOME ; COMPLETE CHLOROPLAST GENOME ; TRANSFER-RNA GENES ; NDH GENES ; OXIDATIVE STRESS ; SEQUENCE ; PHYLOGENY ; DNA ; EVOLUTION ; PHOTOSYNTHESIS
WOS类目	Genetics & Heredity
WOS研究方向	Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/363314
作者单位	[Scobeyeva, Victoria A.] Lomonosov Moscow State Univ, Dept Evolut, Fac Biol, Moscow, Russia; [Scobeyeva, Victoria A.; Belenikin, Maxim S.] Moscow Inst Phys & Technol, Dept Mol & Biol Phys, Dolgoprudnyi, Russia; [Artyushin, Ilya V.] Lomonosov Moscow State Univ, Dept Vertebrate Zool, Fac Biol, Moscow, Russia; [Krinitsina, Anastasiya A.; Speranskaya, Anna S.] Lomonosov Moscow State Univ, Dept Higher Plants, Fac Biol, Moscow, Russia; [Nikitin, Pavel A.] Lomonosov Moscow State Univ, Fac Bioengn & Bioinformat, Moscow, Russia; [Antipin, Maxim I.; Kuptsov, Sergei V.] Lomonosov Moscow State Univ, Bot Garden, Fac Biol, Moscow, Russia; [Omelchenko, Denis O.] Inst Informat Transmiss Problems, Lab Plant Genom, Moscow, Russia; [Logacheva, Maria D.] Skolkovo Inst Sci & Technol, Ctr Life Sci, Moscow, Russia; [Konorov, Evgenii A.] Russian Acad Sci RAS, Vavilov Inst Gen Genet, Lab Anim Genet, Moscow, Russia; [Samoilov, Andrey E.; Speranskaya, Anna S.] Cent Res Inst Epidemiol, Grp Genom & Postgen Technol, Moscow, Russia
推荐引用方式 GB/T 7714	Scobeyeva, Victoria A.,Artyushin, Ilya V.,Krinitsina, Anastasiya A.,et al. Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions[J],2021,12.
APA	Scobeyeva, Victoria A..,Artyushin, Ilya V..,Krinitsina, Anastasiya A..,Nikitin, Pavel A..,Antipin, Maxim I..,...&Speranskaya, Anna S..(2021).Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions.FRONTIERS IN GENETICS,12.
MLA	Scobeyeva, Victoria A.,et al."Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions".FRONTIERS IN GENETICS 12(2021).