目的 解析各5个产地的小构树Broussonetia monoica和藤构Broussonetia kaempferi的叶绿体基因组序列特征与系统进化关系。方法 基于深圳华大BGISEQ-500测序平台，对各5个产地的小构树和藤构个体进行高通量基因组重测序。采用GetOrganelle、Geneious Prime、CpGAVAS2、MISA、REPuter、IRscope、DnaSP、CodonW、IQ-tree等生物信息学工具，进行叶绿体基因组组装与注释、比较基因组分析、密码子偏好分析和系统发育分析。结果 小构树和藤构的各5个体完整叶绿体基因组均呈现典型的环状四分体结构，序列全长分别为160 799～160 877 bp和160 414～160 622 bp，均注释得到135个基因，包括87个蛋白质编码基因、37个tRNA基因、8个rRNA基因和3个假基因。10个叶绿体基因组序列边界基因较为保守，扩张收缩现象不明显。从它们的叶绿体基因组中分别鉴定出98～101个和108～115个SSR位点，以及42～48个和43～54个长重复序列。小构树中的psbC（8 bp）＋psbC_trnS-UGA区域以及atpF、ndhF、ndhI基因和藤构中的ccsA（35 bp）＋ccsA_ndhD区域以及rps16、psbI、petG基因变异度最大。两者叶绿体基因组中均发现30个高频密码子，并筛选出7个相同的最优密码子。系统发育分析显示，小构树与藤构的亲缘关系较构树更近，种内小构树和藤构个体之间的亲缘关系与地理位置有关。结论 小构树和藤构的叶绿体基因组结构、基因数量和密码子使用偏好保守性高，但在重复序列和基因间隔区上存在较大变异；以叶绿体基因数据构建的系统发育树指示了2个物种种内的亲缘关系与样本取样地地理位置有关。

Objective To analysis the characteristics of chloroplast genome sequences and the phylogenetic relationships of Broussonetia Broussonetia kazinoki and Broussonetia kaempferi, utilizing samples from five distinct provenances of each species. Methods High-throughput genome resequencing was conducted on individuals of B. kazinoki and B. kaempferi from five each different provenances using BGISEQ-500 sequencing platform. The chloroplast genomes were assembled and annotated, followed by comparative genomic analysis, codon usage preference analysis, and phylogenetic analysis using bioinformatics tools such as GetOrganelle, Geneious Prime, CpGAVAS2, MISA, REPuter, IRscope, DnaSP, CodonW, and IQ-tree. Results The complete chloroplast genomes of each five individuals from B. kazinoki and B. kaempferi exhibited the typical quadripartite circular structure, with total lengths of 160 799—160 877 bp for B. kazinoki and 160 414—160 622 bp for B. kaempferi. A total of 135 genes were annotated for both species, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and three pseudogenes. The boundary genes of 10 chloroplast genome sequences were relatively conserved, with no distinct expansion or contraction detected. In B. kazinoki, a total of 98—101 SSRs and 42—48 long sequence repeats were identified, while B. kaempferi showed 108—115 SSRs and 43—54 long sequence repeats. The highest levels of sequence variation were observed in the psbC (8 bp) + psbC_trnS-UGA sequence, as well as in the atpF, ndhF, and ndhI genes for B. kazinoki . In contrast, B. kaempferi exhibited variation in the ccsA (35 bp) + ccsA_ndhD sequence, as well as in the rps16, psbI, and petG genes. Additionally, 30 high-frequency codons were shared between the chloroplast genomes of both species, and seven identical optimal codons were identified. Phylogenetic analysis indicated that B. kazinoki was more closely related to B. kaempferi than to B. papyrifera. Furthermore, intraspecific relationships within B. kazinoki and B. kaempferi were found to correlate with geographical origin.Conclusion The chloroplast genome structure, gene number, and codon usage preference of B. kazinoki and B. kaempferi were highly conserved; however, there were substantial variations in repeated sequences and intergenic regions. The phylogenetic tree constructed using chloroplast genome database indicated that the genetic relationships within these two species correlated with the geographical locations of the samples.

R286.2

国家自然科学基金项目（31800309）；温州市基础性公益科研项目（N20240014）；浙江省自然科学基金项目（LY21C030002）