Abstract
Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.
Highlights
The plastid genome, or plastome, in land plants is generally conserved in length, structure, and gene content (Wicke et al, 2011)
Among those assemblies that did not produce consistent results across the different assembly strategies, the large single copy (LSC), the small single copy (SSC), and two inverted repeat (IR) regions were identified in the final Fast-Plast contig and NOVOPlasty assemblies, and the circular plastome was assembled by hand using Geneious v11.1.5
Notwithstanding, the structural parts of the plastome (LSC-IR-SSC) and expected genes could be identified in all output files, final assemblies were constructed by hand
Summary
The plastid genome, or plastome, in land plants is generally conserved in length, structure, and gene content (Wicke et al, 2011). Typical flowering plant plastomes range from 120 to 160 kb, contain 100–120 unique genes, and have a quadripartite structure of two single copy regions (LSC and SSC) separated by two copies of the inverted repeat (IRs) (Jansen & Ruhlman, 2012; Smith & Keeling, 2015). The greatly reduced plastomes of Pilostyles range from 11–15 kb and contain only seven functioning genes (Arias-Agudelo et al, 2019). Plastomes deviating from the quadripartite structure have been reported, either without one copy of the IR (Wojciechowski et al, 2000; Sanderson et al, 2015) or incorporating the entire SSC into the inverted repeats (Sinn et al, 2018)
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