Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)

Abstract

BackgroundPectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton.ResultsWe identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively. These PEL genes were classified into five subfamilies (I-V). Members from the same subfamilies showed relatively conserved gene structures, motifs and protein domains. An analysis of gene chromosomal locations and gene duplication revealed that segmental duplication likely contributed to the expansion of the GhPELs. The 2000 bp upstream sequences of all the GhPELs contained auxin response elements. A transcriptomic data analysis showed that 62 GhPELs were expressed in various tissues. Notably, most (29/32) GhPELs of subfamily IV were preferentially expressed in the stamen, and five GhPELs of subfamily V were prominently expressed at the fiber elongation stage. In addition, qRT-PCR analysis revealed the expression characteristics of 24 GhPELs in four pollen developmental stages and significantly different expression of some GhPELs between long- and short-fiber cultivars. Moreover, some members were responsive to IAA treatment. The results indicate that GhPELs play significant and functionally diverse roles in the development of different tissues.ConclusionsIn this study, we comprehensively analyzed PELs in G. hirsutum, providing a foundation to better understand the functions of GhPELs in different tissues and pathways, especially in pollen, fiber and the auxin signaling pathway.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5047-5) contains supplementary material, which is available to authorized users.

Identification of candidate genes for key fibre‐related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions

“…qFL‐A03‐1 , detected in four environments, overlapping with qFS‐A03‐1 , qFU‐A03‐1 and qBW‐A03‐1 in Cluster‐A03‐1, was positioned at 75.3–84.5 Mb on A03, where a pectate lyase gene ( PEL6 , Gh_A03G1147 ), responsible for degrading pectin (Sun et al ., ), was located. The RNA‐seq data and RT‐qPCR results indicated that Gh_A03G1147 was relatively highly expressed during the earlier stages (0 and 5 DPA) of fibre development and had significantly higher expression in LMY22 than in LY343.…”

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum

“…The RD22-like, PG1β-like and BURP VIII subfamilies were composed of BURP members from monocots and dicots, indicating that these genes might have originated before the divergence of monocots and dicots [10, 12]. However, the members of other subfamilies were only from investigated monocots (BURP VI and BURP VII) or dicots (USP-like, BNM2-like and BURP V subfamilies), indicating that these genes might evolve separately and perform different functions between monocots and dicots [9, 13, 45]. Some results were different from previous studies due to the different methods and species used in the phylogenetic analysis.…”

“…Multiple sequence alignment was performed using identified BURP proteins with ClustalX 2.0. The locations of conserved BURP domains and potential signal peptides of these proteins were determined using SMART database and SignalP 4.0 server (http://www.cbs.dtu.dk/services/SignalP/), respectively [45, 62].…”

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton

“…The multiple sequences of GhWAKs and five AtWAKs (AT1G21210.1, AT1G21230.1, AT1G21240.1, AT1G21250.1 and AT1G21270.1) were aligned using ClustalX 2.0 [ 63 ], and an unrooted phylogenetic tree was generated using the NJ method in MEGA 7.0 [ 64 ].…”