Identification and Characterization of TALE Homeobox Genes in the Endangered Fern Vandenboschia speciosa

Abstract

We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of seven three amino acid loop extension (TALE) homeobox genes (four KNOTTED-like homeobox (KNOX) and three BEL1-like homeobox (BELL) genes) identified after next generation sequencing (NGS) and assembly of the sporophyte and gametophyte transcriptomes of the endangered fern species Vandenboschia speciosa. Among the four KNOX genes, two belonged to the KNOX1 class and the other two belonged to the KNOX2 class. Analysis of the deduced amino acid sequences supported the typical domain structure of both types of TALE proteins, and the homology to TALE proteins of mosses, lycophytes, and seed plant species. The expression analyses demonstrate that these homeodomain proteins appear to have a key role in the establishment and development of the gametophyte and sporophyte phases of V. speciosa lifecycle, as well as in the control of the transition between both phases. Vandenboschia speciosa VsKNAT3 (a KNOX2 class protein) as well as VsBELL4 and VsBELL10 proteins have higher expression levels during the sporophyte program. On the contrary, one V. speciosa KNOX1 protein (VsKNAT6) and one KNOX2 protein (VsKNAT4) seem important during the development of the gametophyte phase. TALE homeobox genes might be among the key regulators in the gametophyte-to-sporophyte developmental transition in regular populations that show alternation of generations, since some of the genes analyzed here (VsKNAT3, VsKNAT6, VsBELL4, and VsBELL6) are upregulated in a non-alternating population in which only independent gametophytes are found (they grow by vegetative reproduction outside of the range of sporophyte distribution). Thus, these four genes might trigger the vegetative propagation of the gametophyte and the repression of the sexual development in populations composed of independent gametophytes. This study represents a comprehensive identification and characterization of TALE homeobox genes in V. speciosa, and gives novel insights about the role of these genes in fern development.

De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

“…Thus, Tables S2 and S3 contain those transcripts that are homologous to genes involved in the vegetative to reproductive transition in flowering plants (487 transcripts) and those homologous to genes involved in the genetic control of plant development in flowering plants (5968 transcripts). Additionally, Table S4 lists the transcripts representing transcription factors (1084 transcripts), with special interest in those that regulate plant development such as MADS box or Homeobox genes [ 48 , 49 ].…”

Genome-wide Identification and Expression Analysis of TALE Gene Family in Pomegranate (Punica granatum L.)

“…In addition, it regulated tomato fruit development [28]. Currently, the TALE gene family has been found in many plants: 33 AtTALE genes in A. thaliana, 40 LjTALE genes in Lotus japonicas K. [63], 46 GaTALE genes in Gossypium arboretum L., 47 GrTALE genes in G. raimondii L., 88 GbTALE genes in G. barbadense L., 94 GhTALE genes G. hirsutum L. [8], and 35 PtTALE genes in poplar [64], 7 VsTALE genes in Vandenboschia speciose G. [16]. Therefore, the copy number of the TALE gene family in different species is different.…”

“…Except for some homeobox genes, TALE encodes an atypical structure forming two helices and three additional amino acid residues (P-Y-P) [9][10][11]. The TALE family plays a vital role in regulating plant growth and development [12][13][14][15], regulating the sporophyte program [16], the formation of plant meristems [7], and the maintenance of organ morphology [17], organ position [18], hormone regulation [19], signal transduction [20] and tuber formation [21]. Studies have shown that BELL and KNOX proteins specifically recognize and bind to form the BELL-KNOX heterodimer protein [22], which is essential for the nuclear localization of two transcription factor proteins and the activity of binding target gene [23,24].…”

Genome-Wide Identification, Expression Profiling and Protein-Protein Interaction Properties of the BEL-Like Homeodomain Gene Family in Apple

“…The homeobox gene is a transcriptional regulator that encodes the homeodomain (HD), which is widely found in eukaryotes. The typical HD consists of 60 amino acids, which can form a 3-helical domain in space [1][2][3]. However, there are some exceptions, such as the TALE (Three Amino-acid Loop Extension) gene families, which encode an atypical DNA binding domain consisting of 63 amino acids, with three additional amino acid residues (P-Y-P) inserted between the first and second helices [3].…”

“…sativum, Medicago truncatula, Camellia chekiangoleosa and five legume species[2][3][4][5][32][33][34][35][36]. Extensive studies have shown that gene replication, including tandem, fragment and genome-wide replication, not only plays an important role in genome rearrangement and amplification, but also in gene function diversification and gene families expression[37].…”