Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Abstract

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

“…WGS, followed by the use of assembly tools, has resulted in an effective manner to obtain chloroplast genomes for different families of angiosperms [ 13 , 31 , 32 , 33 ], as well as of different Magnoliaceae species [ 40 , 41 , 42 , 44 ]. In this study, the plastomes of 15 Neotropical Magnolia species were assembled through the use of short Illumina reads and the GetOrganelle assembler.…”

“…In most plants, this strategy generally results in a much higher proportion of plastome reads compared to other regions of the genome because of the high molarity of these organelles in each cell. This strategy was effective in several plant groups [ 5 , 15 , 28 , 29 , 30 ] and has been applied in studies that use chloroplast genomes to solve evolutionary questions in different angiosperm clades [ 13 , 31 , 32 , 33 ]. Most attention has focused on sequencing crop genomes, and there is little information on wild groups.…”

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

“…6 B). These results indicate that these regions evolve rapidly in the genus Viola , as well as in other related Malpighiales species [ 73 ].…”

A comparative plastomic analysis ofZiziphus jujubavar.spinosa(Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube

“…The chloroplast is a plant organelle originating from a primitive cyanobacterium and performs a fundamental role in plant photosynthesis and other functions ( Gray and Doolittle 1982 ; Timmis et al . 2004 ; Zhou et al . 2021 ).…”