Gene Loss and Evolution of the Plastome

Abstract

Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.

Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)

“…Nuclear genomic data would be useful to investigate whether the genes absent from the plastid have been integrated into the nucleus or have simply been lost. Being similar to ndh genes, rps16 is another commonly lost plastid gene (Mohanta et al., 2020). In the case of rps16 , we argue that after its pseudogenization at the base of Gentianinae, its complete loss in some lineages (which are mostly those variable in plastome structure) should be considered as a simple loss.…”

“…The ndh genes produce the NADH complex, which is essential for electron cycling in photosystem I under heat‐stressed conditions (Wang et al., 2006). Since ndh is often the first gene family to be lost in the process of plastid degradation (Mohanta et al., 2020), studying it contributes to our understanding of the early stages of degradation that are likely to occur in many plant lineages. Eleven ndh genes are present in nearly all flowering plant species studied to date, as compared to 150–200 in the cyanobacterial plastid ancestors.…”

“…Eleven ndh genes are present in nearly all flowering plant species studied to date, as compared to 150-200 in the cyanobacterial plastid ancestors. ndh genes have been lost in nonphotosynthetic parasites due to a relaxation of selective constraints (Barrett et al, 2014;Wicke et al, 2016), but independent losses have also occurred in a minority of photosynthetic plant lineages (Mohanta et al, 2020;Ruhlman et al, 2015), such as in Gnetales and other conifers (Braukmann et al, 2009), Alismatales (Ross et al, 2016), orchids (Kim et al, 2019;Lin et al, 2017), and Geraniaceae (Ruhlman & Jansen, 2018). Ndh may be uniformly lost in a lineage or show a more dynamic fate with presence/absence (or pseudogenization) among populations or closely related species (Barrett et al, 2018;Kim et al 2019).…”

The Genomic Impact of Mycoheterotrophy in Orchids

“…The gene losses observed in the mycoheterotrophic orchids reflect the evolution of their plastomes: massive gene loss restricted to photosynthetic pathways and functions. The only genes retained in their plastid genomes have non-photosynthetic functions ( Graham et al, 2017 ; Barrett et al, 2019 ; Mohanta et al, 2020 ). By extension to the nuclear genome, we can assume that the orthologs not detected in mycoheterotrophic species are probably exclusively associated with photosynthesis, while the conserved orthologs probably have non-photosynthetic functions.…”

The Chloroplast Genome Evolution of Venus Slipper (Paphiopedilum): IR Expansion, SSC Contraction, and Highly Rearranged SSC Regions

“…The plastome size of Pelargonium transvaalense is 242,575 bp, with an IR region of 87,724 bp [6]. On the other hand, IR region loss has been detected in all lineages across land plants [7]. High throughout sequencing provides a good opportunity to test the plastome evolution in more groups.…”