The chloroplast (cp) is critical for various biological functions in plants, such as photosynthesis and stress responses, with its genome offering simpler analysis and sequencing due to its size and reduced homologous influence. This genome's stability and unique features have made it essential for species identification and understanding plant phylogeny. In the context of Carya illinoinensis, or pecan, a key nut crop in China, there's an observed pollination deficiency exacerbated by the timing of pollen release in cultivars like 'Pawnee'. Recent research has expanded to include the cp genomes of various C. illinoinensis cultivars, aiding in the understanding of genetic variations and relationships within the Carya species.
Fruit Research published online a paper entitled "Chloroplast genome sequencing of Carya Illinoinensis cv. Xinxuan-4, a new pecan pollinated cultivar" on 07 March 2024. This study focuses on sequencing the 'Xinxuan-4' cp genome, aiming to address the genetic gap and contribute to the broader research on pecan cultivar genetics and their implications for pollination efficiency and species diversity.
To be specific, this study meticulously sequenced the cp genome of the C. illinoinensis cultivar 'Xinxuan-4', uncovering a genome length of 160,819 base pairs, mirroring that of other cultivars such as 'Pawnee' and 'Lakota'. It had a common quadripartite structure with one large single-copy (LSC), one small single-copy (SSC), and two inverted repeats (IR), displaying genetic stability across the Carya species. The genome contained 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes, with a GC content of 36.1%. Comparative analyses reveal gene variations and codon preference nuances, highlighting evolutionary adaptation through gene gain or loss, such as the absence of the rps12 and rps16 genes in certain cultivars. This study also delves into repeat sequences and chloroplast simple sequence repeats (CpSSRs), identifying 278 SSRs predominantly of the A/T type, indicative of high polymorphism within the species. The investigation of IR contraction and expansion offers insights into structural genome variations, while a comparative genomic structure analysis using the mVISTA program reveals high sequence similarities among the cp genomes of different Carya cultivars, with certain non-coding regions showing divergence.
The selection pressure analysis suggests a mix of purifying and positive selection across various genes, implying adaptive genetic evolution within the species. Nucleotide variability analysis reveals low diversity in the Carya species, aiding in the identification of molecular markers for genetic studies. Phylogenetic analysis positions 'Xinxuan-4' closely with 'Pawnee', indicating a shared maternal lineage possibly originating from North America.
To summarize, this study not only enriches the genetic database for Carya species but also enhances understanding of their evolutionary dynamics, gene expression regulation, and potential for breeding and conservation strategies.
