"Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages"

NonDarwinian Transposable Elements (TE) working with epigenetic GC bias and Codon bias can cause rapid adaptation and change through deep history. TE's are present at the base of the "Bush of Life." As such they represent computer code subroutines that can reprogram themselves and the rest of the genome. Epigenetics guides this to react to the changing environment over the life of our planet.

What could cause these initial pieces of code knowing all the contingencies to come over 4.5 billion years?

The article "Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages" by Chen et al. (2023) investigates the evolution of the tubby-like protein (TLP) gene family in seven representative Poaceae lineages. The TLP gene family is essential for growth and development in plants and animals. Previous studies have shown that the TLP gene family has evolved through a variety of mechanisms, including whole-genome duplication (WGD), dispersed duplication (DSD), and transposed duplication (TRD).

In this study, Chen et al. used a variety of methods, including phylogenetic analysis, gene expression analysis, and protein structure analysis, to investigate the evolution of the TLP gene family in the seven Poaceae lineages. They found that the TLP gene family has evolved through a complex process involving multiple duplication events. WGD was the most important duplication event, but DSD and TRD also played a significant role.

The authors also found that the evolution of the TLP gene family has been affected by a variety of selective pressures. Duplication events have created new opportunities for adaptive evolution, and the authors found evidence of positive selection in several TLP genes. However, they also found evidence of purifying selection in other TLP genes, suggesting that these genes are essential for plant growth and development.

Overall, this study provides a comprehensive overview of the evolution of the TLP gene family in Poaceae. The authors' findings suggest that the TLP gene family has evolved through a complex process involving multiple duplication events and a variety of selective pressures. This study provides new insights into the evolution of this important gene family and its role in plant growth and development.

Here are some of the key findings of the study:

The TLP gene family has evolved through a complex process involving multiple duplication events.
WGD was the most important duplication event, but TRD (Transposable Elements) also played a significant role. TE's have been OVERLOOKED as Junk DNA.
The evolution of the TLP gene family has been affected by a variety of selective pressures, including GC bias and Codon bias both epigenetic phenomena.
This study provides new insights into the evolution of the TLP gene family and its role in plant growth and development.

Article snippets:

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

Abstract

In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.

Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research.

Conclusions

This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

Introduction

Genes can be duplicated through a variety of mechanisms, including whole-genome duplication (WGD), tandem duplication (TD), proximal duplication (PD), dispersed duplication (DSD), and transposed duplication (TRD).

the origin of duplication of a gene can belong to only one of the five duplication types and does not allow a gene to originate through different duplication mechanisms

There are five types of gene duplication mechanisms: WGD, TD, PD, DSD, and TRD

(TRD) was missing in the above studies

TRD often leads to the formation of pseudogenes

TRD can occur through DNA-based or RNA-based mechanisms.

Although there are many methods and tools available to perform gene duplication origin analysis [4, 11,12,13], they do not identify all types of duplication origin due to algorithmic limitations. This may be the reason for the phenomenon of incomplete conclusions.

we hypothesize that the origin of duplication of TLP genes may include TRD

our results showed that the evolution of TLP genes was also affected by TRD, as we hypothesized

The number of TRD pairs was greater than the number of WGD pairs in maize and barley

In general, WGD occurred later than TRD and DSD, with DSD occurring somewhat earlier

Thus, the grass species that we studied exhibit a “consistent shrinking” evolutionary pattern.

DNA-based mechanisms occur by relocating the copied gene or gene fragment to a new chromosomal locus via DNA transposons

RNA-based transposed duplication works by reverse transcription of spliced messenger RNA to produce a single-exon retrocopy from a multi-exon parental gene.

The new retrogene is deposited in a new chromosomal environment with new (i.e., nonancestral) neighbouring genes

The evolution of TLP genes was influenced not only by whole-genome duplication and dispersed duplication but also by transposed duplication

inferred transposon-mediated gene duplication tends to reduce gene expression levels

We found that TLP genes are subject to TRD, and therefore, this may affect TLP gene expression.

Codon usage bias has been hypothesized by some to have contributed to adaptive gene evolution

we found that the codon biases of the TLP gene family were consistent across the seven grass species.

previous research findings have shown that GC content elevation results in codon usage bias

The majority of the optimal codons of the grass TLP family contain GC bases, which may be evidence that codon usage bias is related to GC content.

Conclusions

we supported our conjecture that TLP genes originated from TRD in addition to the previously reported WGD and DSD.

What could cause these initial pieces of code knowing all the contingencies to come over 4.5 billion years?

Here are some of the key findings of the study:

The TLP gene family has evolved through a complex process involving multiple duplication events.
WGD was the most important duplication event, but TRD (Transposable Elements) also played a significant role.
The evolution of the TLP gene family has been affected by a variety of selective pressures, including GC bias and Codon bias both epigenetic phenomena.
This study provides new insights into the evolution of the TLP gene family and its role in plant growth and development.