南京林业大学学报(自然科学版) ›› 2024, Vol. 48 ›› Issue (4): 25-36.doi: 10.12302/j.issn.1000-2006.202205003
所属专题: 专题报道Ⅰ:郑万钧先生诞辰120周年纪念专题Ⅱ
• 专题报道Ⅰ:郑万钧先生诞辰120周年纪念专题Ⅱ(执行主编 曹福亮、尹佟明、李维林、方升佐) • 上一篇 下一篇
收稿日期:
2022-05-02
修回日期:
2022-06-10
出版日期:
2024-07-30
发布日期:
2024-08-05
通讯作者:
*陈昕(chenxinzhou@njfu.edu.cn),教授。作者简介:
马建慧(2556429572@qq.com)。
基金资助:
MA Jianhui(), CHEN Xin*(), GENG Liyang, TANG Chenqian, WEI Xueyan
Received:
2022-05-02
Revised:
2022-06-10
Online:
2024-07-30
Published:
2024-08-05
摘要:
【目的】明晰花楸属白毛系(Sorbus ser. Folgnerianae)是否为单系,重建该系3种棕脉花楸(S. dunnii)、石灰花楸(S. folgneri)和江南花楸(S. hemsleyi)的系统发生关系。【方法】通过标本查阅和野外观察比较白毛系的叶、花、果特征;基于新增的白毛系种和大果花楸(S. megalocarpa,冠萼组Sect. Aria)4种5个样本的质体基因组序列特征、重复序列和序列变异,结合花楸属已发表物种的数据,以蔷薇科其他属代表种和Barbeya oleoides为外类群,分析白毛系的系统发生关系。【结果】白毛系3种在花柱数目、花药颜色、果实形态及花萼是否宿存等方面差异显著,易于鉴别。5个样本的质体基因组具有相似的结构、基因含量和组成。质体基因组长度为159 898~160 755 bp,GC含量为36.4%~36.6%。均注释到113个Unique基因(79个蛋白编码基因、30个tRNA基因、4个rRNA基因),且IR区具扩展长度不等的rps19Ψ和ycf1Ψ 2个假基因。检测到的48~54条SSRs、36~49条散在重复序列和20个高分化度的非编码区可为花楸属物种的群体遗传学、谱系地理学和系统发生研究提供分子标记。基于ML/BI树的系统发生分析结果显示花楸属为复系,6个组各自形成单系;白毛系的3种虽然聚为一组,但水榆花楸(S. alnifolia,直脉系Ser. Alnifoliae)同棕脉花楸、石灰花楸的亲缘关系较江南花楸更近。【结论】白毛系不为单系,形态特征和质体基因组分析为理解白毛系的系统发生提供了有效途径。
中图分类号:
马建慧,陈昕,耿礼阳,等. 蔷薇科花楸属白毛系的系统发生分析[J]. 南京林业大学学报(自然科学版), 2024, 48(4): 25-36.
MA Jianhui, CHEN Xin, GENG Liyang, TANG Chenqian, WEI Xueyan. Phylogenetic analysis of Sorbus ser. Folgnerianae (Rosaceae)[J].Journal of Nanjing Forestry University (Natural Science Edition), 2024, 48(4): 25-36.DOI: 10.12302/j.issn.1000-2006.202205003.
表1
花楸属白毛系3种及大果花楸采集信息及登录信息"
种名species | 采集地 location | 地理坐标 geographical coordinates | 海拔/m altitude | 采集时间 (年-月-日) collection time (year-month-day) | 采集人及凭证标本 collector and voucher | GenBank登录号 GenBank accession number |
---|---|---|---|---|---|---|
棕脉花楸 S. dunnii | 安徽黄山 | 118°10'15.96″E, 30°6'58.38″N | 1 186 | 2019-05-20 | 陈昕、李嘉宝,1430 | OK054488 |
石灰花楸 S. folgneri | 湖北兴山 | 110°29'46.97″E, 31°19' 05.16″N | 1 789 | 2016-05-24 | 陈昕、洑香香、刘清亮,0506 | ON262428 |
石灰花楸 S. folgneri | 四川都江堰 | 103°19'45.68″E, 29°32'50.47″N | 1 163 | 2021-04-23 | 朱大海,2000 | ON262429 |
江南花楸 S. hemsleyi | 湖北神农架 | 110°18'30.14″E, 31°35'55.67″N | 1 830 | 2016-05-25 | 陈昕、洑香香、刘清亮,0522 | OQ100083 |
大果花楸 S. megalocarpa | 四川龙苍沟 | 102°53'13.75″E, 29°37'48.37″N | 1 358 | 2021-03-21 | 胡太伦,1992 | ON259046 |
表2
白毛系3种及大果花楸5个样本质体基因组基本特征"
样本 sample | 大小/bp plastome length | 大单拷贝 区长度/ bp LSC length | 小单拷贝 区长度/ bp SSC length | 反向区 长度/bp IR length | 编码区 长度/% coding regions length | 非编码区 长度/% noncoding regions length | GC含量/% GC content | unique 基因数 unique genes | unique 蛋白编码 基因数 unique CDS | tRNA 总数 total tRNA | rRNA 总数 total rRNA | 基因 总数 total genes | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
总计 total | LSC | SSC | IR | CDS | rRNA | tRNA | |||||||||||||||
棕脉花楸 S. dunnii | 160 280 | 88 053 | 19 409 | 26 409 | 56.43 | 43.57 | 36.5 | 34.2 | 30.3 | 42.6 | 37.7 | 55.6 | 53.3 | 113 | 79 | 30 | 4 | 132 | |||
石灰花楸 S. folgneri (ON262428) | 160 631 | 88 333 | 19 480 | 26 409 | 56.32 | 43.68 | 36.4 | 34.1 | 30.2 | 42.6 | 37.7 | 55.6 | 53.3 | 113 | 79 | 30 | 4 | 132 | |||
石灰花楸 S. folgneri (ON262429) | 160 755 | 88 483 | 19 454 | 26 409 | 56.26 | 43.74 | 36.4 | 34.1 | 30.3 | 42.6 | 37.7 | 55.6 | 53.3 | 113 | 79 | 30 | 4 | 132 | |||
江南花楸 S. hemsleyi | 160 527 | 88 415 | 19 304 | 26 404 | 56.34 | 43.66 | 36.4 | 34.1 | 30.3 | 42.7 | 37.7 | 55.6 | 53.3 | 113 | 79 | 30 | 4 | 132 | |||
大果花楸 S. megalocarpa | 159 868 | 87 713 | 19 335 | 26 410 | 56.58 | 43.42 | 36.6 | 34.3 | 30.3 | 42.7 | 37.7 | 55.6 | 53.3 | 113 | 79 | 30 | 4 | 132 |
表3
白毛系3种及大果花楸质体基因组基因名称及功能分类"
基因功能 function | 基因分类 gene type | 基因名称 gene | 基因数量 number of genes |
---|---|---|---|
自我复制 self replication | rRNA | rrn4.5a、rrn5a、rrn16a、rrn23a | 4 |
tRNA | trnA-UGC*a、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、 trnfM-CAU、trnG-UCC*、trnG-GCC、trnH-GUG、trnI-CAUa、 trnI-GAU*a、trnK-UUU*、trnL-CAAa、trnL-UAA*、trnL-UAG、 trnM-CAU、trnN-GUUa、trnP-UGG、trnQ-UUG、trnR-ACGa、 trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、 trnV-GACa、trnV-UAC*、trnW-CCA、trnY-GUA | 30 | |
核糖体小亚基 ribosomal proteins(SSU) | rps2、rps3、rps4、rps7a、rps8、rps11、rps12*a、 rps14、rps15、rps16*、rps18、rps19/rps1 | 12 | |
核糖体大亚基 ribosomal proteins(LSU) | rpl2*a、rpl14、rpl16*、rpl20、rpl22、 rpl23a、rpl32、rpl33、rpl36 | 9 | |
RNA聚合酶亚基 RNA polymerase | rpoA、rpoB、rpoC1*、rpoC2 | 4 | |
光合作用 genes for photosynthesis | 光合系统Ⅰ photosystemⅠ | psaA、psaB、psaC、psaI、psaJ, | 5 |
光合系统Ⅱ photosystemⅡ | psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、 psbJ、psbK、psbL、psbM、psbN、psbT、psbZ | 15 | |
细胞色素复合物 cytochrome b/f complex | petA、petB*、petD*、petG、petL、petN | 6 | |
ATP合成酶 ATP synthase | atpA、atpB、atpE、atpF*、atpH、atpI | 6 | |
NADH脱氢酶 subunits of NADH-dehydrogenase | ndhA*、ndhB*a、ndhC、ndhD、ndhE、 ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK | 11 | |
二磷酸核酮糖羧化酶大亚基 rubiscoCO large subunit | rbcL | 1 | |
其他基因 hypothetical chloroplast reading frames | 乙酰 CoA 羧化酶 subunit of Acetyl-CoA-carboxylase | accD | 1 |
膜包被蛋白基因 envelop membrane protein gene | cemA | 1 | |
c型细胞色素合成基因 c-type cytochrom synthesis gene | ccsA | 1 | |
蛋白酶基因 protease gene | clpP** | 1 | |
成熟酶基因 maturase gene | matK | 1 | |
翻译起始因子 translation initiation factor | infA | 1 | |
未知功能 unknow function | 假定的质体读码框 hypothetical chloroplast reading frames | ycf1/ycf | 4 |
图3
白毛系3种及大果花楸6样本重复序列分析 a.不同SSRs类型的数量 number of SSRs in different types;b.SSRs在基因间区、内含子区、外显子区的分布数量 number of SSRs in IGS, intron and exon regions;c.SSRs在LSC、SSC、IR区的分布数量 number of SSRs in the LSC, SSC and IR;d.不同重复序列类型的分布数量 number of different types of repeats sequence;e.不同重复序列长度的分布数量 number of different length of repeats sequence。"
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