The complete chloroplast genome of Agave fourcroydes.

Agave fourcroydes (henequen) is the only cultivated Agave species in the Yucatan Peninsula, which is mainly used for fiber production. In the present study, we have successfully assembled the chloroplast (cp) genome of A. fourcroydes. The full length of the cp genome is 157,291 bp with a GC content at 37.8%. The cp genome is constructed with an inverted repeat region a (IRa) of 26,573 bp, a small single copy region (SSC) of 18,230 bp, an inverted repeat region b (IRb) of 26,573 bp and a large single copy region (LSC) of 85,915 bp. The annotation result reveals 132 genes on the cp genome, including 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic tree reveals that A. fourcroydes is closely related with A. sisalana.

Agave fourcroydes Lemaire 1864 (henequen) is the only cultivated Agave species in the Yucatan Peninsula, which is mainly used for fiber production (Colunga-Garcíamarín et al. 1999; Piven et al. 2001). There are a large amount of leaf juice and fibrous waste after fiber extraction. It has been reported that the leaf juice of A. fourcroydes could be used as feedstock for ethanol production, which makes it of great potential in warming and drying regions around the world (Cáceres-Farfán et al. 2008; Yang et al. 2015). Till now, a series of studies have revealed the phylogenetic relationships of more than 37 Agave species (Huang et al. 2018; Jiménez-Barron et al. 2020). However, the phylogenetic relationship and systematic position of A. fourcroydes still remain ambiguous at the chloroplast (cp) genome level. Thus, we conducted the Illumina sequencing work for the assembly of its cp genome, with the purpose to reveal its systematic position and benefit future studies on Agave cp.

The young leaves of A. fourcroydes were cut from a three-year-old plant from the germplasm garden of Guangxi Subtropical Crops Research Institute, Nanning, China (22.90°N, 108.33°E). The specimen was deposited in Herbarium of Guangxi Subtropical Crops Research Institute (http://www.gxrzs.com/, Tao Chen, 15607718198@wo.cn) under the voucher number HGS-jm2020012. The leaves were ground in liquid nitrogen for the extraction of total genomic DNA by the modified CTAB method (Doyle and Doyle 1987). DNA sample was used for library construction and Illumina sequencing in Biozeron Biotech (Shanghai, China). The Illumina NovaSeq platform was selected for paired-end short reads sequencing, which generated a total of 5.28 Gb raw data. The raw data was submitted to SRA under the accession of PRJNA705498. The cp genome was assembled with the NOVOPlasty software and then gap filled with the GapCloser software (Luo et al. 2012; Dierckxsens et al. 2017). The cp genome was further annotated and corrected by DOGMA and Geneious v11.0.3, respectively (Wyman et al. 2004; Kearse et al. 2012). The full cp genome sequence of A. fourcroydes was submitted to GenBank under the accession of MW540496.

The full length of the assembled A. fourcroydes cp genome is 157,291 with a GC content at 37.84%. The cp genome contain four sequence regions, including IRa (26,573 bp), IRb (26,573 bp), SSC (18,230 bp) and LSC (85,915 bp). The annotation result reveals 132 genes on the cp genome, including 86 protein-coding genes, 38 tRNAs and 8 rRNAs.

We selected a total of 29 cp genome sequences for phylogenetic analysis. Among these, there are 26 species in Agavoideae and 3 other species (Albuca kirkii, Nolina atopocarpa and Oziroe biflora) as outgroup (McKain et al. 2016; Lee et al. 2019; Jin et al. 2020). These full sequences were aligned by the MAFFT software (Katoh and Standley 2013). After which, a maximum likelihood phylogenetic tree was constructed by MEGA7 software with bootstrap values of 1000 replicates (Kumar et al. 2016). The result revealed that A. fourcroydes is closely related with A. sisalana (Figure 1). This study would expand the number of plant chloroplast genomes and benefit future studies related to Agave chloroplast.

Figure 1.

Phylogenetic tree of 29 chloroplast genomes.