Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

Abstract

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.

Peer Review #2 of "The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography (v0.1)"

“…The cp genomes of most angiosperms are validated to contain approximately 130 genes, of which about 20 genes have two copies in two IRs, leaving the rest 110 being unique genes (Mader et al, 2018;Hu et al, 2017;Xu et al, 2017;Yang et al, 2018). Our annotations are similar to those reported above.…”

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

“…Khakhlova & Bock (2006) suggested that gene divergence with less variability in the IR and coding regions may be a result of copy corrections during gene conversion, which can correct or delete the mutation. Codons were shown to have a strong tendency toward A or U at the third codon position, which is similar to the expression of an A/U ending in other plants (Gao et al, 2017;Clegg et al, 1994;Mader et al, 2018;Meng et al, 2018). This phenomenon may explain why the Adenine-Thymine (AT) content is slightly higher than the GC content in the cp genome of Dicliptera.…”

“…The chloroplast genome (cp genome) is an independent genome that has been used in many evolutionary studies (Fan et al, 2018;Gao, Wang & Deng, 2018;George et al, 2015;Chen et al, 2018;Inkyu et al, 2018;Kim & Lee, 2004;Wang et al, 2016;Mader et al, 2018;Meng et al, 2018;Ma et al, 2017;Raubeson et al, 2007;Wang et al, 2008;Wu et al, 2018). It has a simple structure with a low molecular weight and multiple copies.…”

“…Most of the cp genomes have circular structures with quadripartite organizations composed of one large single copy region (LSC), one small single copy region (SSC), and a pair of inverted regions (IRs). However, there are numerous exceptions to the common structure, like the IR-lacking clade (IRLC) in Fabaceae (Fan et al, 2018;Gao, Wang & Deng, 2018;George et al, 2015;Chen et al, 2018;Inkyu et al, 2018;Kim & Lee, 2004;Wang et al, 2016;Mader et al, 2018;Meng et al, 2018;Schwarz et al, 2015). The complete cp genomes of more than 2,400 plants have been published, to date, in the NCBI database (http://www.ncbi.nlm.nih.gov/genome).…”

Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

“…Due to the lack of recombination, small genome size and high copy number per cell [3,4], complete chloroplast genome sequences have been extensively used in phylogenetics analysis and species identi cation [5,6]. The results showed that the chloroplast genome contains additional information to improve phylogenetic analysis [7][8][9][10][11]. Comparative chloroplast genome sequences provide an opportunity to discover the sequence variation and identify mutation hotspot regions, while also detecting the gene loss and duplication events.…”