# Advances in Genome Sequencing and Natural Rubber Biosynthesis in Rubber-Producing Plants
## 2 Progress in the Genome Sequencing of Rubber-Producing Plants  
Progress in researching and understanding the mechanism of NR biosynthesis has been slow, failing to keep pace with the rapidly growing global demand for industrial NR consumption. One important reason for this is the lack of high-quality genomic information. The genome sequencing progress of rubber-producing plants is summarized in Table 1. In 2013, the draft genome of the rubber tree (RRIM600) was first sequenced using a whole-genome shotgun approach, with an assembled 2.15 Gb genome [20]. A total of 68,955 predicted genes were identified, including the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity. In 2016, two rubber tree genomes, RRIM600 and Reyan7-33-97, were reported, with their genome sizes being significantly reduced to 1.55 Gb and 1.47 Gb, respectively [21,22]. This reduction was achieved through the integration of Illumina sequencing data with either PacBio or BAC clone sequencing data. Both studies discovered that the capacity of _H. brasiliensis_ to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes as well as the high expression of these genes in latex. In 2017, the genome of the BPM24 clone was assembled using Illumina short reads and PacBio long-read data [23]. Notably, a long-range \"Chicago\" assembly technique was employed to scaffold the preliminary assembly, resulting in 1.26 Gb of assembled sequences. Moreover, 363 Mb sequences of the genome were mapped to 18 linkage groups by using an SNP-based genetic map. In 2020, the first chromosome-level genome of the rubber tree cultivar GT1 was assembled using single-molecule real-time sequencing (SMRT) and chromosome conformation capture (Hi-C) technologies [24]. The GT1 genome has a size of 1.47 Gb, and it is estimated to contain 44,187 protein-coding genes. Additionally, this study has identified numerous candidate domestication genes involved in rubber biosynthesis between cultivated and wild rubber trees. In 2023, a high-quality, chromosome-level genome sequence of the wild rubber tree (MT/VB/25A 57/8) was reported by combining Illumina sequencing data, SMRT sequencing data, Bio-Nano data, and Hi-C data [25]. A total of 35,318 predicted protein-coding genes were identified from the 1.72 Gb genome sequences. Furthermore, the population genomic analysis found 361 selection signatures that align with 245 genes and 155 significant markers associated with latex yield that correspond to 326 candidate genes. During the same year, a high-quality genome of the elite rubber tree cultivar CATAS8-79 was assembled by integrating PacBio CLR sequencing data, Hi-C data, and Bio-Nano data [26]. The CATAS8-79 genome has a size of 1.58 Gb, with 1.55 Gb assigned to 18 chromosomes, indicating a remarkably high level of sequence continuity. A total of 38,595 high-confidence gene models were predicted and functionally annotated in the CATAS8-79 genome. The continuous improvement in genomic integrity has not only facilitated the genome-assisted selection breeding of rubber trees but also expedited the domestication of other rubber-producing plants. The first draft genome of TKS (TK1151) was reported in 2017, with an assembled 1.29 Gb genome predicted to contain 46,731 protein-coding genes, including 102 candidate genes involved in the NR biosynthesis pathway [15]. Following that, the genome was significantly improved by integrating PacBio SMRT sequencing, Bio-Nano optical mapping, and Hi-C technologies, thereby generating a more continuous genome of 1.07 Gb in 2021 [27]. Furthermore, through the comparison of the _T. mongolicum_ (TM5) genome, a species closely related to TKS, gene family expansion events were identified in the NR biosynthesis pathway in TK1151. The genome of lettuce was assembled in 2017 using the Illumina whole-genome shotgun method [16]. The assembly comprises 2.38 Gb and encompasses 38,919 gene models, covering approximately 88% of the estimated genome size.