The complete chloroplast genome of Myriophyllum spicatum reveals a 4‐kb inversion and new insights regarding plastome evolution in Haloragaceae

Abstract

Myriophyllum, among the most species‐rich genera of aquatic angiosperms with ca. 68 species, is an extensively distributed hydrophyte lineage in the cosmopolitan family Haloragaceae. The chloroplast (cp) genome is useful in the study of genetic evolution, phylogenetic analysis, and molecular dating of controversial taxa. Here, we sequenced and assembled the whole chloroplast genome of Myriophyllum spicatum L. and compared it to other species in the order Saxifragales. The complete chloroplast genome sequence of M. spicatum is 158,858 bp long and displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) region from the small single copy (SSC) region. Based on sequence identification and the phylogenetic analysis, a 4‐kb phylogenetically informative inversion between trnE‐trnC in Myriophyllum was determined, and we have placed this inversion on a lineage specific to Myriophyllum and its close relatives. The divergence time estimation suggested that the trnE‐trnC inversion possibly occurred between the upper Cretaceous (72.54 MYA) and middle Eocene (47.28 MYA) before the divergence of Myriophyllum from its most recent common ancestor. The unique 4‐kb inversion might be caused by an occurrence of nonrandom recombination associated with climate changes around the K‐Pg boundary, making it interesting for future evolutionary investigations.

The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae

“…In addition, the results of IRscope analysis reveal no obvious expansion or contraction of the chloroplast IR region. Furthermore, although a recent study has identified a unique 4-kb inversion in the chloroplast genome of the outgroup species Myriophyllum spicatum (Liao et al, 2020), our analyses show a high degree of similarity in chloroplast gene order between Crassulaceae and the outgroup species Penthorum chinense.…”

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

“…The new plastid genomes sequenced in this study have no evidence of any structural rearrangements, underlining the strong conservatism of plastid genome structure in Saxifragales [20,23] (the rare exception is Haloragaceae, distantly related to taxa discussed here; see [23,24]). Other than Saniculiphyllum, we found no evidence at the DNA sequence level for pseudogenes beyond those previously documented for Saxifragales [20,23] and many other angiosperms, namely ycf15 and pseudogenes created by IR (inverted repeat) region boundaries within ycf1 and ycf2 (cf.…”

Plastome structure and phylogenetic relationships of Styracaceae (Ericales)

“…Plastid structure is usually conserved in most angiosperms, but large inversions have been detected in many taxa. For example, a 4-kb inverted fragment in the LSC between rpoB-trnT was found in Myriophyllum spicatum [ 56 ], and a large gene inversion has also found in Lotus japonicas , Arabidopsis thaliana [ 57 ] and members of Oleaceae [ 58 ]. Because of their scarcity, plastid inversions are of great value to the study of genome evolution [ 59 , 60 ].…”