The Complete Chloroplast Genomes Of Lauraceae Species: Comparative Genomic And Phylogenetic Analyses

Lauraceae is a large family of woody plants(except the genus Cassytha being herbaceous)composed of 50 genera and 3000 species,which is widely distributed in Old World tropical to subtropical evergreen broad-leaved forests and New World moist forests.Lauraceae species have high economic value and are widely used in construction,industry,cosmetic,pharmaceutical and food industry.However,Lauraceae is a group with complex evolution and controversial classification,among which there are divergences on the systematic position of the controversial genera(Actinodaphne and Sassafras)and the establishment of tribe Cinnamoneae.Chloroplast genome has the characters of small scale,uniparental inheritance,low nucleotide substitution rate and highly conservative,which is widely used in plant phylogeny.Inflorescence type,as the important morphological character of Lauraceae,can be used to solve taxon problems.In this study,chloroplast genome sequences of 15 species within 5 genera of Lauraceae were sequenced and assembled.And we combined the chloroplast genomes of 20 species within 19 genera of Lauraceae from NCBI were used for comparative genomics;Phylogenetic trees of 133 Lauraceae species were constructed based on chloroplast genomes and common protein coding genes;Based on the inflorescence types and chloroplast genomes,the framework of Lauraceae tribes was raised.And we infered the inflorescence evolution.The main contents and results are as follows:(1)Lauraceae species' chloroplast genomes are relatively conservative,with a pair of inverted repeats,a large single copy region and a small single copy region,except Cassytha species have no inverted repeats.The genome sizes depend on the expansion,contraction or loss of the IR region.The chloroplast genomes of Lauraceae are highly conservative,without major gene rearrangement or inversion events and have similar codon bias.Sequence difference indicated that the chloroplast genomes of Lauraceae evolved independently with different loss patterns,and rpl2 gene loss and ndh gene loss or pseudogene in some genera were important evolutionary events in Lauraceae.(2)We developed 15 chloroplast hypervariable regions,which can be used as molecular markers to study population genetics and phylogeny,including 5 coding regions(rps15,ccs A,ycf2,rps19,mat K)and 10 intergenic spacer(Intron trn V-UAC,trn H-psb A,trn D-trn Y,trn T-trn L,trn S-trn G,rpl32-trn L,psa C-ndh E,psb M-trn D,trn P-psa J,rps4-trn T).(3)Based on the chloroplast genome of 133 species within 24 genera of Lauraceae,the phylogenetic tree of Lauraceae was constructed.Combined with inflorescence type analysis,the results showed that Lauraceae could be divided into 7 clades,corresponding to 7 tribes.Laurus-Neolitsea clade corresponded to Laureae(umbels with alternate opposite involucres),Cinnamomum-Ocotea clade corresponded to Cinnamoneae(panicles with spiral bracts),Machilus-Persea clade corresponded to Perseeae(panicles without involucre,3-floret cymes strictly symmetrical),Caryodaphnopsis clade corresponded to Caryodaphnopsideae,Neocinnamomum clade corresponded to Neocinnamomeae,Cassytha clade corresponded to Cassytheae,Beilschmiedia-Cryptocarya clade corresponded to Cryptocaryeae(irregular panicles,the two flowers of lateral branch are not strictly symmetrical).(4)According to the traditional classification system of Lauraceae and the related molecular phylogeny in recent years,combined with the analysis of inflorescence types,This study supported the establishment of tribe Cinnamoneae including Sassafras,Cinnamomum and Nectandra;the genera Actinodaphne was classified into tribe Laureae.(5)Based on Sassafras tzumu's inflorescence morphology and cross section of secondary inflorescence axis with secondary branching flowers and single flower,combined with the relationship between inflorescence types and phylogeny,we speculated the evolution direction of Lauraceae's inflorescence: the two flowers in secondary inflorescence axis of panicle degenerated or aborted,forming highly reduced panicle(pseudo-raceme),and the inflorescence axis shortened continuously to form umbel.The reason may be related to the change of climate and environment when Lauraceae plants expanded from subtropical and tropical regions to temperate regions.