Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum)

Abstract

Flax (Linum usitatissimum L.) is a valuable food and fiber crop cultivated for its quality fiber and seed oil. α-, β-, γ-tubulins and actins are the main structural proteins of the cytoskeleton. α- and γ-tubulin and actin genes have not been characterized yet in the flax genome. In this study, we have identified 6 α-tubulin genes, 13 β-tubulin genes, 2 γ-tubulin genes, and 15 actin genes in the flax genome and analyzed the phylogenetic relationships between flax and Arabidopsis thaliana tubulin and actin genes. Six α-tubulin genes are represented by three paralogous pairs, among 13 β-tubulin genes 7 different isotypes can be distinguished, 6 of which are encoded by two paralogous genes each. γ-tubulin is represented by a paralogous pair of genes one of which may be not functional. Fifteen actin genes represent seven paralogous pairs-seven actin isotypes and a sequentially duplicated copy of one of the genes of one of the isotypes. Exon-intron structure analysis has shown intron length polymorphism within the β-tubulin genes and intron number variation among the α-tubulin gene: three or four introns are found in two or four genes, respectively. Intron positioning occurs at conservative sites, as observed in numerous other plant species. Flax actin genes show both intron length polymorphisms and variation in the number of intron that may be two or three. These data will be useful to support further studies on the specificity, functioning, regulation, and evolution of the flax cytoskeleton proteins.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

“…Earlier, Bhattacharya et al (2000) reported only 1-2 copy of actin genes in green algae and 2-3 copies in bryophyta species. However, consistent with our analysis recent genome wide studies have reported 21 actin genes in maize, 15 actin genes in flax (Slajcherová et al 2012, Pydiura et al 2018. Further, our pairwise analysis showed that 10-13 rice actin gene homologs were present in twenty animal species, 10-12 homologs in seven fungal and four Protista species.…”

A Journey Through Plant Cytoskeleton: Hot Spots in Signaling and Functioning

“…In the paper of Pydiura et al () genome‐wide identification, phylogenetic classification, and exon‐intron structure characterization of the tubulin and actin genes in flax ( Linum usitatissimum ) are considered. Besides β‐tubulin genes, α‐ and γ‐tubulin and actin genes have not been characterized yet in the flax genome (Gavazzi et al, ).…”

Ist and IIIrd intron length polymorphism of actin genes as a tool for flax DNA-profiling

“…Результати та обговорення У попередній роботі нами опубліковані дані щодо біоінформаційного пошуку генів актину, закодованих у геномі льону-довгунця [15]. Результати оцінки особливостей екзон-інтронної структури 15-ти відібраних генів актину льону свідчать про те, що більшість їх мають 4 консервативні ділянки -екзони та 3 гіперваріабельні -інтрони.…”