The actin multigene family in Populus: organization, expression and phylogenetic analysis

Abstract

Despite the significance of actin in plant growth and development, little is known of the structure, expression and evolution of the actin gene family in woody plants. In this study, we systematically examined the diversification of the actin gene family in Populus by integrating genomic organization, expression, and phylogeny data. Genome-wide analysis of the Populus genome indicated that actin is a multigene family consisting of eight members, all predicted to encode 377-amino acid polypeptides that share high sequence homology ranging from 94.2 to 100% identity. Microarray and real-time PCR expression analysis showed that the PtrACT family members are differentially expressed in different tissues, exhibiting overlapping and unique expression patterns. Of particular interest, all PtrACT genes have been found to be preferentially expressed in the stem phloem and xylem, suggesting that poplar PtrACTs are involved in the wood formation. Gene structural and phylogenetic analyses revealed that the PtrACT family is composed of two main subgroups that share an ancient common ancestor. Extremely high intraspecies synonymous nucleotide diversity of pi(syn) = 0.01205 was detected, and the pi(non-syn)/pi(syn) ratio was significantly less than 1; therefore, the PtACT1 appears to be evolving in Populus, primarily under purifying selection. We demonstrated that the actin gene family in Populus is divided into two distinct subgroups, suggesting functional divergence. The results reported here will be useful in conducting future functional genomics studies to understand the detailed function of actin genes in tree growth and development.

Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus

“…Then, psRNATarget analysis (Dai and Zhao, 2011) (http://plantgrn.noble.org/psRNATarget/) was performed on a P. trichocarpa genomic library for the prediction of Pto-miR257 putative target genes via complementary base pairing interactions. Each of the 12 potential targets that have high or differential abundance in stem was cloned and sequenced by amplification from the genomic DNA of the 40 individuals of P. tomentosa, using the PCR method described in Zhang et al (2010) (Supplementary Table S1 and Supplementary Data S2). All genomic DNA sequences were submitted to GenBank and the accession numbers are shown in Supplementary Table S1.…”

“…The amplification reactions were performed as described by Zhang et al (2010) for target genes. For Pto-miR257, reactions were carried out according to Song et al (2013).…”

Molecular characterization, tissue expression profile, and single nucleotide polymorphism analysis of the periostin gene in swine

“…Total RNA was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) from the longissimus dorsi muscle of 25-day-old Yorkshire pigs (Zhang et al, 2010). RNA was treated with DNase I (Liang and Pardee, 1992) and then reverse-transcribed with Moloney Murine Leukemia Virus reverse transcriptase (Promega, Madison, WI, USA).…”

“…Total RNA was isolated from 10 tissues (heart, liver, spleen, lung, kidney, intestine, cecum, pancreas, crureus, and longissimus dorsi muscle) of a 25-day-old weaned Yorkshire piglet and a Shaziling piglet of the same age (Winer et al, 1999;Zhang et al, 2010). The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as an internal control.…”

Molecular characterization and tissue expression profile of porcine Ephrin-B2

“…Total RNA was reverse transcribed by M-MLV reverse transcriptase (Promega, Madison, WI, USA), oligo dT primer, and ribonuclease inhibitor in a total volume of 50 µL. The PCR conditions were as follows: 5 min at 95°C, then 35 cycles of 30 s at 95°C, 30 s at 55°C, 60 s at 72°C (Zhang et al, 2010). Primers were designed based on the conserved sequences using the software Primer premier 5.0 as shown in Table 1.…”