Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

Abstract

Background Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. Methods The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. Results The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.

Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences

“…The expanded regions appeared as unalignable insertions, where the number of indels are correlated with the length of the non-coding regions ( Supplementary Table 7 ). Furthermore, other studies have proposed that repeat sequences lead to plastome expansion; however, the expansion of these species is also associated with gene duplications caused by boundary shifts in IR regions, e.g., watercress ( Yan et al, 2019 ) and Rhododendron delavayi ( Li H. et al, 2020 ). Interestingly, short palindromic repeats (20–25 bp) are prevalent in the plastomes of C. subtropicum and C. tibeticum ( Supplementary Table 5 ).…”

“…The average chloroplast genome (plastome) size of land plants is 151 kb, with most species ranging from 130–170 kb in length, and the average GC content is 36.3% (NCBI database, 4,281 land plant plastomes, March 17, 2020) ( Supplementary Table 1 ). However, previous studies documented that the plastome size of some lineages was extremely enlarged ( Chumley et al, 2006 ; Kim et al, 2015 ; Blazier et al, 2016 ; Weng et al, 2017 ; Lim et al, 2018 ; Gruzdev et al, 2019 ; Li H. et al, 2020 ). The largest chloroplast genome of angiosperm is Pelargonium transvaalense (242, 575 bp), with the inverted repeat (IR) region of the species expanding to 87,724 bp ( Weng et al, 2017 ).…”

“…Of more than 4,000 land plant plastomes from NCBI, 82 sequences examined to date had chloroplast genome sizes over 170 kb, and seven of these species had chloroplast genome sizes over 200 kb ( Supplementary Table 1 ). The expansion of the plastomes of these species is mainly caused by gene duplications in the IR regions ( Chumley et al, 2006 ; Weng et al, 2017 ; Sinn et al, 2018 ; Li H. et al, 2020 ) or the expansion of repeat sequences in non-coding regions ( Dugas et al, 2015 ; Li H. et al, 2020 ).…”

“…However, the short-reads method occasionally does not perform well owing to biased coverage depth, which may lead to fragmented genome assemblies ( Ferrarini et al, 2013 ; Sinn et al, 2018 ). Recently, a few studies used long reads ( Ferrarini et al, 2013 ; Wu et al, 2014 ; Chen et al, 2015 ; Xiang et al, 2016 ; Cauzsantos et al, 2017 ; Lee et al, 2020 ; Zhang et al, 2020 ) or combined short and long reads for chloroplast genome assembly ( Ruhlman et al, 2017 ; Lin et al, 2018 ; Wang et al, 2018 ; Yan et al, 2019 ; Li H. et al, 2020 ). Ruhlman et al (2017) combined long and short read data to investigate repeat sequences in Monsonia emarginata (Geraniaceae).…”

Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

“…cordata cp genome were used to construct their phylogenetic relationship. Only the homologous CDs were used to construct the phylogenetic relationship to reduce data redundancy, such as that done in the study of Rhododendron delavayi [ 32 ]. A total of 75 homologous CDs (coding gene sequence) were employed in this study, including psbB , psbZ , ndhF , petG , rps18 , rpoB , petN , psbA , psaJ , ccsA , rpoC1 , rbcL , psbM , ndhG , rps19 , rpl2 , psbL , psaC , rps3 , matK , psbE , rpl14 , petA , rpl33 , psaA , rpl36 , ndhK , ndhJ , psbK , atpI , psbF , psbI , rps2 , rpl32 , atpH , psbN , accD , psaB , rps11 , atpA , rps14 , infA , psaI , ycf1 , rps4 , atpE , psbJ , rpl16 , rps15 , rpl20 , rpoA , ndhD , psbH , rpoC2 , ndhI , ndhA , ndhH , rps16 , atpB , petD , psbC , ndhB , petB , atpF , rps7 , rpl23 , psbD , clpP , rpl22 , ndhE , petL , psbT , ycf2 , rps12 , and ndhC , were used to determine the phylogenetic relationship.…”